June 2017 Archives by thread

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Starting: Thu Jun 1 05:36:54 CEST 2017
Ending: Fri Jun 30 22:21:31 CEST 2017
Messages: 873

• [gmx-users] REMD analysis of trajectories   YanhuaOuyang
  • [gmx-users] REMD analysis of trajectories   Mark Abraham
    • [gmx-users] REMD analysis of trajectories   YanhuaOuyang
      • [gmx-users] REMD analysis of trajectories   Mark Abraham
      • [gmx-users] REMD analysis of trajectories   Smith, Micholas D.
• [gmx-users] tetrahedral order parameter   ISHRAT JAHAN
  • [gmx-users] tetrahedral order parameter   Justin Lemkul
    • [gmx-users] tetrahedral order parameter   ISHRAT JAHAN
      • [gmx-users] Fwd: tetrahedral order parameter   ISHRAT JAHAN
• [gmx-users] Reg: creation of separate chains in .pdb file   Syed Azeem
  • [gmx-users] Reg: creation of separate chains in .pdb file   Justin Lemkul
• [gmx-users] "cmake" failed to install   ZHANG Cheng
  • [gmx-users] "cmake" failed to install   mario at exactas.unlpam.edu.ar
    • [gmx-users] "cmake" failed to install   ZHANG Cheng
      • [gmx-users] "cmake" failed to install   Mark Abraham
      • [gmx-users] "cmake" failed to install   mario at exactas.unlpam.edu.ar
      • [gmx-users] "cmake" failed to install   ZHANG Cheng
    • [gmx-users] "cmake" failed to install   Mark Abraham
  • [gmx-users] "cmake" failed to install   Mark Abraham
• [gmx-users] Doubt about gmx wham analysis   Justin Lemkul
  • [gmx-users] Doubt about gmx wham analysis   Varvdekar Bhagyesh Rajendra
    • [gmx-users] Doubt about gmx wham analysis   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about gmx wham analysis   Justin Lemkul
      • [gmx-users] Doubt about gmx wham analysis   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about gmx wham analysis   Justin Lemkul
• [gmx-users] Deuterium Order Parameter Calculations   Justin Lemkul
• [gmx-users] DrudeFF topology transfer from CHARMM to GROMACS   Tomasz Piskorz
• [gmx-users] System volume "jumps" on exact continuations   Mark Abraham
  • [gmx-users] System volume "jumps" on exact continuations   Elizabeth Ploetz
    • [gmx-users] System volume "jumps" on exact continuations   Mark Abraham
      • [gmx-users] System volume "jumps" on exact continuations   Elizabeth Ploetz
• [gmx-users] How to perform final MD simulation after extending a NPT simulation   Mark Abraham
• [gmx-users] gmx freevolume   Mark Abraham
• [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?   Mark Abraham
  • [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?   Erik Marklund
    • [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?   Mark Abraham
      • [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?   Erik Marklund
      • [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?   Justin Lemkul
• [gmx-users] Analysis   RAHUL SURESH
  • [gmx-users] Fwd: Analysis   RAHUL SURESH
  • [gmx-users] Analysis   Mark Abraham
• [gmx-users] AMBER LIPID14 ff in GROMACS   Mark Abraham
  • [gmx-users] AMBER LIPID14 ff in GROMACS   Amit Singh
    • [gmx-users] AMBER LIPID14 ff in GROMACS   Justin Lemkul
    • [gmx-users] AMBER LIPID14 ff in GROMACS   Christopher Neale
• [gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy   Christopher Neale
  • [gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy   Mark Abraham
• [gmx-users] Simulated annealing   Mark Abraham
• [gmx-users] System volume "jumps" on exact continuations   Elizabeth Ploetz
• [gmx-users] Disparity in total energy between consecutive steps   Felix Y Yang
• [gmx-users] System volume "jumps" on exact continuations   Elizabeth Ploetz
  • [gmx-users] System volume "jumps" on exact continuations   Szilárd Páll
    • [gmx-users] System volume "jumps" on exact continuations   Elizabeth Ploetz
• [gmx-users] gmx trjconv -center -boxcenter zero isn't amazing at putting the selection at (0, 0, 0), but I don't know why   Christopher Neale
  • [gmx-users] gmx trjconv -center -boxcenter zero isn't amazing at putting the selection at (0, 0, 0), but I don't know why   Christopher Neale
• [gmx-users] How to calculate number of cholesterol molecules   Archana Sonawani-Jagtap
  • [gmx-users] How to calculate number of cholesterol molecules   Justin Lemkul
    • [gmx-users] How to calculate number of cholesterol molecules   Antonio Baptista
• [gmx-users] Umbrella sampling and PMF calculations   Alex
  • [gmx-users] Umbrella sampling and PMF calculations   Justin Lemkul
    • [gmx-users] Umbrella sampling and PMF calculations   Alex
      • [gmx-users] Umbrella sampling and PMF calculations   Justin Lemkul
      • [gmx-users] Umbrella sampling and PMF calculations   Alex
      • [gmx-users] Umbrella sampling and PMF calculations   Justin Lemkul
      • [gmx-users] Umbrella sampling and PMF calculations   Alex
      • [gmx-users] Umbrella sampling and PMF calculations   Alex
      • [gmx-users] Umbrella sampling and PMF calculations   Justin Lemkul
      • [gmx-users] Umbrella sampling and PMF calculations   Alex
      • [gmx-users] Umbrella sampling and PMF calculations   Justin Lemkul
      • [gmx-users] Umbrella sampling and PMF calculations   Alex
• [gmx-users] charmm36 lipid forcefield error   Archana Sonawani-Jagtap
  • [gmx-users] charmm36 lipid forcefield error   Justin Lemkul
    • [gmx-users] charmm36 lipid forcefield error   Archana Sonawani-Jagtap
      • [gmx-users] charmm36 lipid forcefield error   Justin Lemkul
• [gmx-users] How to conserve total energy from a position-restrained step to a non-constrained step   Felix Y Yang
• [gmx-users] How to improve the performance of simulation in HPC (finding optimal number of nodes and processors)   Santhosh Kumar Nagarajan
  • [gmx-users] How to improve the performance of simulation in HPC (finding optimal number of nodes and processors)   Smith, Micholas D.
  • [gmx-users] How to improve the performance of simulation in HPC (finding optimal number of nodes and processors)   Szilárd Páll
• [gmx-users] destruction of the structure of a molecule in water after energy minimization   Saeed Nasiri
  • [gmx-users] destruction of the structure of a molecule in water after energy minimization   Justin Lemkul
• [gmx-users] Perturbation Thermodynamic Integration   Hannes Loeffler
• [gmx-users] Problem with center-of-mass RDF and subsequent coordination number calculation   Apramita Chand
  • [gmx-users] Fwd: Problem with center-of-mass RDF and subsequent coordination number calculation   Apramita Chand
  • [gmx-users] Problem with center-of-mass RDF and subsequent coordination number calculation   André Farias de Moura
• [gmx-users] Peptide out of box even after applying trjconv   Apramita Chand
  • [gmx-users] Fwd: Peptide out of box even after applying trjconv   Apramita Chand
    • [gmx-users] Fwd: Peptide out of box even after applying trjconv   Justin Lemkul
• [gmx-users] Interpretation of RMSD matrix   Apramita Chand
  • [gmx-users] Interpretation of RMSD matrix   Mark Abraham
• [gmx-users] Randomly replace molecules with another molecule   Li, Shi
  • [gmx-users] Randomly replace molecules with another molecule   Justin Lemkul
• [gmx-users] Using SLLOD to find Viscosity   nishi kashyap
  • [gmx-users] Using SLLOD to find Viscosity   David van der Spoel
    • [gmx-users] Using SLLOD to find Viscosity   nishi kashyap
      • [gmx-users] Using SLLOD to find Viscosity   David van der Spoel
      • [gmx-users] Using SLLOD to find Viscosity   nishi kashyap
• [gmx-users] Calculation of nematic order parameter using gromacs   nidhi sorout
  • [gmx-users] Calculation of nematic order parameter using gromacs   Antonio Baptista
  • [gmx-users] Calculation of nematic order parameter using gromacs   André Farias de Moura
    • [gmx-users] Calculation of nematic order parameter using gromacs   nidhi sorout
      • [gmx-users] Calculation of nematic order parameter using gromacs   André Farias de Moura
      • [gmx-users] Calculation of nematic order parameter using gromacs   nidhi sorout
• [gmx-users] using the Fourier function for dihedral in the OPLS FF   Saeed Nasiri
  • [gmx-users] using the Fourier function for dihedral in the OPLS FF   Justin Lemkul
• [gmx-users] Error with dihedral type 5   Matteo Busato
• [gmx-users] using the Fourier function for dihedral in the OPLS FF   Saeed Nasiri
• [gmx-users] RMSD Matrix error   Apramita Chand
  • [gmx-users] RMSD Matrix error   Mark Abraham
• [gmx-users] EM error   ‪Mohammad Roostaie‬ ‪
• [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box   Apramita Chand
  • [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box   André Farias de Moura
    • [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box   Mark Abraham
• [gmx-users] Negative deuterium order parameters   Poncho Arvayo Zatarain
• [gmx-users] QM/MM with Orca   Marcos Veríssimo Alves
• [gmx-users] Fwd: Lysosyme in water   shivanigupta.gupta6 at gmail.com
  • [gmx-users] Fwd: Lysosyme in water   RAHUL SURESH
  • [gmx-users] Fwd: Lysosyme in water   Ommair Ishaque
  • [gmx-users] Fwd: Lysosyme in water   Ommair Ishaque
  • [gmx-users] Fwd: Lysosyme in water   Ommair Ishaque
• [gmx-users] Doubt from Graphene oxide layer   Rakesh Pant
  • [gmx-users] Doubt from Graphene oxide layer   RAHUL SURESH
• [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 27   Apramita Chand
• [gmx-users] Segmentation fault (core dumped) Too many LINCS warnings   Deepesh Sigdel
• [gmx-users] Significance of box vectors in GRO trajectory file.   Dawid das
  • [gmx-users] Significance of box vectors in GRO trajectory file.   Justin Lemkul
    • [gmx-users] Significance of box vectors in GRO trajectory file.   Dawid das
      • [gmx-users] Significance of box vectors in GRO trajectory file.   Justin Lemkul
      • [gmx-users] Significance of box vectors in GRO trajectory file.   Dawid das
• [gmx-users] Generation of density curve for biphasic system   Debraj Das
  • [gmx-users] Generation of density curve for biphasic system   Justin Lemkul
    • [gmx-users] Generation of density curve for biphasic system   Debraj Das
      • [gmx-users] Generation of density curve for biphasic system   Justin Lemkul
• [gmx-users] System Charge   Pandya, Akash
  • [gmx-users] System Charge   Mark Abraham
    • [gmx-users] System Charge   Pandya, Akash
      • [gmx-users] System Charge   Mark Abraham
• [gmx-users] long equilibration for HII phase   Mohsen Ramezanpour
• [gmx-users] Parameters for gram-positive peptidoglycan   Norfarisha Mohd Fadil
• [gmx-users] tMPI error   ‪Mohammad Roostaie‬ ‪
• [gmx-users] RMSD analysis   RAHUL SURESH
  • [gmx-users] RMSD analysis   Justin Lemkul
    • [gmx-users] RMSD analysis   RAHUL SURESH
      • [gmx-users] RMSD analysis   Justin Lemkul
      • [gmx-users] RMSD analysis   RAHUL SURESH
      • [gmx-users] RMSD analysis   Justin Lemkul
• [gmx-users] RMSD Matrix Error   Apramita Chand
  • [gmx-users] RMSD Matrix Error   Mark Abraham
• [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)   Apramita Chand
  • [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)   Justin Lemkul
• [gmx-users] metal ions in equilibration step   Mahboobeh Eslami
  • [gmx-users] metal ions in equilibration step   Justin Lemkul
• [gmx-users] mdp options in GROMACS 4.5.5   ‪Mohammad Roostaie‬ ‪
  • [gmx-users] mdp options in GROMACS 4.5.5   João Henriques
    • [gmx-users] mdp options in GROMACS 4.5.5   João Henriques
      • [gmx-users] mdp options in GROMACS 4.5.5   Mark Abraham
      • [gmx-users] mdp options in GROMACS 4.5.5   ‪Mohammad Roostaie‬ ‪
      • [gmx-users] mdp options in GROMACS 4.5.5   Justin Lemkul
• [gmx-users] Fw: mdp options in GROMACS 4.5.5   ‪Mohammad Roostaie‬ ‪
• [gmx-users] Energy Minimisation   Pandya, Akash
  • [gmx-users] Energy Minimisation   Mark Abraham
• [gmx-users] Usage of position restraint during FEP calculation   Геннадий Макаров
  • [gmx-users] Usage of position restraint during FEP calculation   Justin Lemkul
• [gmx-users] Simulation of pure water   G R
  • [gmx-users] Simulation of pure water   Mark Abraham
• [gmx-users] Ramachandran plot   RAHUL SURESH
  • [gmx-users] Ramachandran plot   Mark Abraham
    • [gmx-users] Ramachandran plot   RAHUL SURESH
      • [gmx-users] Ramachandran plot   Mark Abraham
      • [gmx-users] Ramachandran plot   RAHUL SURESH
• [gmx-users] number of coordinates does not match after POSRES   Simon Kit Sang Chu
  • [gmx-users] number of coordinates does not match after POSRES   Mark Abraham
    • [gmx-users] number of coordinates does not match after POSRES   Simon Kit Sang Chu
      • [gmx-users] number of coordinates does not match after POSRES   Justin Lemkul
      • [gmx-users] number of coordinates does not match after POSRES   Simon Kit Sang Chu
      • [gmx-users] number of coordinates does not match after POSRES   Justin Lemkul
      • [gmx-users] number of coordinates does not match after POSRES   Simon Kit Sang Chu
• [gmx-users] Simulation of pure water   G R
  • [gmx-users] mdrun with multi option   Debdip Bhandary
    • [gmx-users] mdrun with multi option   Mark Abraham
      • [gmx-users] mdrun with multi option   Debdip Bhandary
• [gmx-users] IB Workshop: Bio Visualization with Blender and MembraneEditor (Odense 24.6.2017 )   Björn Sommer
• [gmx-users] 3-10 or Pi helices are changing to Alpha over the time: 100 ns MD   prasun kumar
• [gmx-users] Gromacs   saranya
  • [gmx-users] Gromacs   Justin Lemkul
    • [gmx-users] Gromacs   saranya
      • [gmx-users] Gromacs   Justin Lemkul
• [gmx-users] RDF of a group around CNT axis   Sajjad Kavyani
  • [gmx-users] RDF of a group around CNT axis   SRINIVAS MUSHNOORI
    • [gmx-users] RDF of a group around CNT axis   Sajjad Kavyani
      • [gmx-users] RDF of a group around CNT axis   Sajjad Kavyani
• [gmx-users] Doubt about Normal Mode Analysis while scaling nonbonded interactions   Varvdekar Bhagyesh Rajendra
• [gmx-users] Simulate protein at subzero condition in aqueous buffer   ZHANG Cheng
  • [gmx-users] Simulate protein at subzero condition in aqueous buffer   João Henriques
  • [gmx-users] Simulate protein at subzero condition in aqueous buffer   ZHANG Cheng
    • [gmx-users] Simulate protein at subzero condition in aqueous buffer   Justin Lemkul
    • [gmx-users] Simulate protein at subzero condition in aqueous buffer   ZHANG Cheng
      • [gmx-users] Simulate protein at subzero condition in aqueous buffer   João Henriques
      • [gmx-users] Simulate protein at subzero condition in aqueous buffer   João Henriques
      • [gmx-users] Simulate protein at subzero condition in aqueous buffer   ZHANG Cheng
• [gmx-users] gmx insert-molecules   Li, Shi
  • [gmx-users] gmx insert-molecules   Justin Lemkul
• [gmx-users] gmx insert-molecules   Shi Li
  • [gmx-users] gmx insert-molecules   Justin Lemkul
• [gmx-users] Cylinder pulling through bilayer   Gmx QA
  • [gmx-users] Cylinder pulling through bilayer   Gmx QA
• [gmx-users] deltaG shifts in g_wham   Alex
  • [gmx-users] deltaG shifts in g_wham   Justin Lemkul
• [gmx-users] problem with "gmx rdf": It cannot find the center of mass of a reference group   Sajjad Kavyani
  • [gmx-users] problem with "gmx rdf": It cannot find the center of mass of a reference group   Sajjad Kavyani
• [gmx-users] gmx insert-molecules   Shi Li
  • [gmx-users] gmx insert-molecules   Justin Lemkul
• [gmx-users] Remove all but N closest water molecules from protein   Jose Borreguero
• [gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?   Sanim Rahman
  • [gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?   Dallas Warren
• [gmx-users] summary_distances.dat file not complete   Norfarisha Mohd Fadil
  • [gmx-users] summary_distances.dat file not complete   Justin Lemkul
• [gmx-users] Enquiry about simulating the aggregation behavior of bile salts in GROMACS   lxj2586
• [gmx-users] GMX GPU Rest Time   Daniel Kozuch
  • [gmx-users] GMX GPU Rest Time   Mark Abraham
• [gmx-users] Calculating the radius of gyration of clusters   GAYATHRI S
• [gmx-users] Remove all but N closest water molecules from protein   João Henriques
  • [gmx-users] Remove all but N closest water molecules from protein   Mark Abraham
    • [gmx-users] Remove all but N closest water molecules from protein   João Henriques
      • [gmx-users] Remove all but N closest water molecules from protein   Mark Abraham
      • [gmx-users] Remove all but N closest water molecules from protein   João Henriques
    • [gmx-users] Remove all but N closest water molecules from protein   Jose Borreguero
• [gmx-users] Lennard Jones and Buckingham potential together in one simulation   Narjes Khosravian
  • [gmx-users] Lennard Jones and Buckingham potential together in one simulation   Mark Abraham
    • [gmx-users] Lennard Jones and Buckingham potential together in one simulation   Narjes Khosravian
      • [gmx-users] Lennard Jones and Buckingham potential together in one simulation   Mark Abraham
• [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 49   ABEL Stephane
• [gmx-users] Reference point of position restraint   Simon Kit Sang Chu
  • [gmx-users] Reference point of position restraint   Mark Abraham
• [gmx-users] LJ-Buckham potential   Narjes Khosravian
• [gmx-users] Doubt regarding enthalpy calculation   Tushar Ranjan Moharana
• [gmx-users] gmx insert-molecules   Shi Li
  • [gmx-users] gmx insert-molecules   Justin Lemkul
• [gmx-users] gmx insert-molecules   Shi Li
  • [gmx-users] gmx insert-molecules   Justin Lemkul
• [gmx-users] Error in deuterium order parameters, index, nr   Poncho Arvayo Zatarain
  • [gmx-users] Error in deuterium order parameters, index, nr   Justin Lemkul
• [gmx-users] Output center of mass of each molecules in a system.   Li, Shi
  • [gmx-users] Output center of mass of each molecules in a system.   Christopher Neale
    • [gmx-users] Output center of mass of each molecules in a system.   Justin Lemkul
• [gmx-users] Doubt about Free Energy Calculations using g_bar   Varvdekar Bhagyesh Rajendra
  • [gmx-users] Doubt about Free Energy Calculations using g_bar   Justin Lemkul
    • [gmx-users] Doubt about Free Energy Calculations using g_bar   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Justin Lemkul
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Justin Lemkul
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Mark Abraham
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Mark Abraham
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Alex
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Justin Lemkul
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy Calculations using g_bar   Justin Lemkul
• [gmx-users] Using PME with Slab Boundaries   Sanim Rahman
• [gmx-users] How to mix Amber FF with Slipid FF   Quyen V. Vu
• [gmx-users] Regarding the forcefield, topology..   Dilip H N
  • [gmx-users] Regarding the forcefield, topology..   Dallas Warren
• [gmx-users] NVT and NPT equilibration   Pandya, Akash
  • [gmx-users] NVT and NPT equilibration   Justin Lemkul
• [gmx-users] Unknown CMake command "tmpi_get_source_list"   Vincenzo Carravetta
  • [gmx-users] Unknown CMake command "tmpi_get_source_list"   Mark Abraham
• [gmx-users] auto correlation function and time   Mohsen Ramezanpour
• [gmx-users] Inserting ionic liquids   Pranesh M
  • [gmx-users] Inserting ionic liquids   Justin Lemkul
• [gmx-users] doubt in RMSD   Seera Suryanarayana
  • [gmx-users] doubt in RMSD   Justin Lemkul
• [gmx-users] NVT and NPT equilibration   Manuel Martinez-Jimenez
• [gmx-users] How to interpret gmx H_bond analysis?   Adarsh V. K.
  • [gmx-users] How to interpret gmx H_bond analysis?   Justin Lemkul
• [gmx-users] Doubt in RMSD   Seera Suryanarayana
  • [gmx-users] Doubt in RMSD   Justin Lemkul
• [gmx-users] System Charge   Quyen V. Vu
  • [gmx-users] System Charge   Justin Lemkul
• [gmx-users] Lenard Jones interaction between two chains   Simon Kit Sang Chu
  • [gmx-users] Lenard Jones interaction between two chains   Justin Lemkul
• [gmx-users] (Newbie) Residue SiO2 for solvation?   Jose Borreguero
  • [gmx-users] (Newbie) Residue SiO2 for solvation?   Justin Lemkul
• [gmx-users] MD Simulation run   Jai Krishna
  • [gmx-users] MD Simulation run   Mark Abraham
• [gmx-users] MD Simulation run   Quyen V. Vu
• [gmx-users] Doubt in RMSD   Seera Suryanarayana
  • [gmx-users] Doubt in RMSD   Justin Lemkul
• [gmx-users] Multinode parallel GPU/CPU Gromacs performance   Petar Zuvela
  • [gmx-users] Multinode parallel GPU/CPU Gromacs performance   Szilárd Páll
• [gmx-users] Regarding the forcefield, topology..   Dilip H N
• [gmx-users] Regarding the forcefield, topology..   petar.zuvela
• [gmx-users] Cyclic Peptide in Cyclohexane - LINCS warnings   Billy Williams-Noonan
  • [gmx-users] Cyclic Peptide in Cyclohexane - LINCS warnings   Billy Williams-Noonan
• [gmx-users] Regarding the forcefield, topology..   Dilip H N
• [gmx-users] extract the coordinate by using traj command for sphere system   gozde ergin
  • [gmx-users] extract the coordinate by using traj command for sphere system   Justin Lemkul
    • [gmx-users] extract the coordinate by using traj command for sphere system   gozde ergin
      • [gmx-users] extract the coordinate by using traj command for sphere system   Justin Lemkul
      • [gmx-users] extract the coordinate by using traj command for sphere system   gozde ergin
• [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings   Billy Williams-Noonan
  • [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings   Mark Abraham
    • [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings   Billy Williams-Noonan
      • [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings   Billy Williams-Noonan
      • [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings   Mark Abraham
      • [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings   Justin Lemkul
      • [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings   Billy Williams-Noonan
      • [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings   Justin Lemkul
• [gmx-users] Snapshots from trajectories   Pandya, Akash
  • [gmx-users] Snapshots from trajectories   Shweta Kumari
  • [gmx-users] Snapshots from trajectories   András Ferenc WACHA
    • [gmx-users] Snapshots from trajectories   Pandya, Akash
• [gmx-users] error in running md.mdp   VARSHA RANI
  • [gmx-users] error in running md.mdp   Justin Lemkul
• [gmx-users] Fwd: Using amber-ff14SB forcefield port to GROMACS - blowing up error   p.kartheek
  • [gmx-users] Fwd: Using amber-ff14SB forcefield port to GROMACS - blowing up error   Mark Abraham
• [gmx-users] Fwd: error in running md.mdp   VARSHA RANI
• [gmx-users] error in running md.mdp   VARSHA RANI
  • [gmx-users] error in running md.mdp   Justin Lemkul
• [gmx-users] GPCR insertion in POPC_Cholesterol bilayer   Archana Sonawani-Jagtap
  • [gmx-users] GPCR insertion in POPC_Cholesterol bilayer   Justin Lemkul
    • [gmx-users] GPCR insertion in POPC_Cholesterol bilayer   Archana Sonawani-Jagtap
• [gmx-users] WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.   Rana Rehan Khalid
  • [gmx-users] WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.   Justin Lemkul
    • [gmx-users] WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.   Rana Rehan Khalid
      • [gmx-users] WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.   Rana Rehan Khalid
      • [gmx-users] WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.   Mark Abraham
• [gmx-users] Pulling COM option   Angela Marcela Murcia Rios
• [gmx-users] How to hold CG bead together   Sheikh Imamul Hossain
  • [gmx-users] How to hold CG bead together   Dallas Warren
• [gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?   petar.zuvela
  • [gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?   Justin Lemkul
• [gmx-users] Regarding hydrogen bond dynamics   Dilip H N
  • [gmx-users] Regarding hydrogen bond dynamics   Justin Lemkul
• [gmx-users] Regarding hydrogen bond dynamics   Dilip H N
• [gmx-users] error in running md   VARSHA RANI
  • [gmx-users] error in running md   Vytautas Rakeviius
  • [gmx-users] error in running md   Mark Abraham
    • [gmx-users] error in running md   VARSHA RANI
      • [gmx-users] error in running md   Justin Lemkul
• [gmx-users] Doubt about g_lie   Varvdekar Bhagyesh Rajendra
  • [gmx-users] Doubt about g_lie   Justin Lemkul
• [gmx-users] defining two interactions potentials for same pair of atoms   Sahithya S Iyer
  • [gmx-users] defining two interactions potentials for same pair of atoms   Mark Abraham
    • [gmx-users] defining two interactions potentials for same pair of atoms   Sahithya S Iyer
• [gmx-users] How to interpret gmx H_bond analysis?   Adarsh V. K.
  • [gmx-users] How to interpret gmx H_bond analysis?   Justin Lemkul
• [gmx-users] How to interpret gmx H_bond analysis?   Adarsh V. K.
• [gmx-users] Pulling COM option   Nikhil Maroli
  • [gmx-users] Pulling COM option   Angela Marcela Murcia Rios
    • [gmx-users] Pulling COM option   Justin Lemkul
      • [gmx-users] Pulling COM option   Angela Marcela Murcia Rios
      • [gmx-users] Pulling COM option   Justin Lemkul
      • [gmx-users] Pulling COM option   Angela Marcela Murcia Rios
• [gmx-users] How to find the loading capacity of a nanostructure?   faride badalkhani
• [gmx-users] How to find the loading capacity of a nanostructure?   faride badalkhani
• [gmx-users] Doubt about Free Energy control Minimization   Varvdekar Bhagyesh Rajendra
  • [gmx-users] Doubt about Free Energy control Minimization   Justin Lemkul
    • [gmx-users] Doubt about Free Energy control Minimization   Varvdekar Bhagyesh Rajendra
    • [gmx-users] Doubt about Free Energy control Minimization   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy control Minimization   Justin Lemkul
      • [gmx-users] Doubt about Free Energy control Minimization   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy control Minimization   Justin Lemkul
      • [gmx-users] Doubt about Free Energy control Minimization   Varvdekar Bhagyesh Rajendra
      • [gmx-users] Doubt about Free Energy control Minimization   Justin Lemkul
      • [gmx-users] Doubt about Free Energy control Minimization   Varvdekar Bhagyesh Rajendra
• [gmx-users] Fatal error: Atom N01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Rana Rehan Khalid
  • [gmx-users] Fatal error: Atom N01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Mark Abraham
• [gmx-users] Ion flux/current   Alex
• [gmx-users] ATB topology: itp to top conversion   Anna Lappala
  • [gmx-users] ATB topology: itp to top conversion   Justin Lemkul
  • [gmx-users] ATB topology: itp to top conversion   Mark Abraham
    • [gmx-users] ATB topology: itp to top conversion   Anna Lappala
• [gmx-users] how to select index group in gmx hbond or any other command   Md. Imrul Reza Shishir
  • [gmx-users] how to select index group in gmx hbond or any other command   Justin Lemkul
• [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Rana Rehan Khalid
  • [gmx-users] Fwd: Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Rana Rehan Khalid
  • [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Justin Lemkul
    • [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Rana Rehan Khalid
      • [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Rana Rehan Khalid
      • [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Mark Abraham
      • [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Rana Rehan Khalid
• [gmx-users] using groups in index for gmx select   Sahithya S Iyer
  • [gmx-users] using groups in index for gmx select   Mark Abraham
• [gmx-users] Ion flux/current   Nikhil Maroli
  • [gmx-users] Ion flux/current   Alex
    • [gmx-users] Ion flux/current   Justin Lemkul
      • [gmx-users] Ion flux/current   Alex
• [gmx-users] Regarding creating the molecules...   Dallas Warren
  • [gmx-users] Regarding creating the molecules...   Dallas Warren
• [gmx-users] how to pull both direction with constant force   Md. Imrul Reza Shishir
• [gmx-users] In vacuo MD   Linus Johannissen
  • [gmx-users] In vacuo MD   Justin Lemkul
    • [gmx-users] In vacuo MD   Linus Johannissen
      • [gmx-users] In vacuo MD   Mark Abraham
• [gmx-users] How to read .dat file   Qing Lv
  • [gmx-users] How to read .dat file   Dd H
    • [gmx-users] How to read .dat file   Qing Lv
• [gmx-users] Can we calculate Potential of mean force from normal MD simulations   Apramita Chand
  • [gmx-users] Can we calculate Potential of mean force from normal MD simulations   André Farias de Moura
• [gmx-users] rectangular box: pressure coupling scaling   Johannes Wagner
  • [gmx-users] rectangular box: pressure coupling scaling   Justin Lemkul
• [gmx-users] Problems with IMD in Gromacs 2016.3   Charles Laughton
  • [gmx-users] Problems with IMD in Gromacs 2016.3   Kutzner, Carsten
    • [gmx-users] Problems with IMD in Gromacs 2016.3   Charles Laughton
      • [gmx-users] Problems with IMD in Gromacs 2016.3   Mark Abraham
      • [gmx-users] Problems with IMD in Gromacs 2016.3   Charles Laughton
      • [gmx-users] Problems with IMD in Gromacs 2016.3   Mark Abraham
• [gmx-users] Alternatives to COMPASS forcefield   Bruno Escribano
  • [gmx-users] Alternatives to COMPASS forcefield   Smith, Micholas D.
• [gmx-users] Simulation of Carbon nanotube   Nikhil Maroli
  • [gmx-users] Simulation of Carbon nanotube   Justin Lemkul
• [gmx-users] bad contacts on lipid tails   Mohsen Ramezanpour
  • [gmx-users] bad contacts on lipid tails   Justin Lemkul
    • [gmx-users] bad contacts on lipid tails   Mohsen Ramezanpour
      • [gmx-users] bad contacts on lipid tails   Justin Lemkul
      • [gmx-users] bad contacts on lipid tails   Mohsen Ramezanpour
      • [gmx-users] bad contacts on lipid tails   Justin Lemkul
      • [gmx-users] bad contacts on lipid tails   Mohsen Ramezanpour
• [gmx-users] Spherical Water Droplet   Shraddha Parate
  • [gmx-users] Spherical Water Droplet   Alex
    • [gmx-users] Spherical Water Droplet   Justin Lemkul
• [gmx-users] Umbrella sampling   Kingsley Theras Primus Dass .
  • [gmx-users] Umbrella sampling   Justin Lemkul
• [gmx-users] RDF OF PROTEIN - LIGAND   Neha Gupta
• [gmx-users] DIHEDRAL SCAN   Neha Gupta
• [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   jay patil
• [gmx-users] pdb2gmx peptide nanotube   Farzane Abasi
• [gmx-users] precision of input gro file   Yu Ogawa
  • [gmx-users] precision of input gro file   Eric Smoll
    • [gmx-users] precision of input gro file   Yu Ogawa
      • [gmx-users] precision of input gro file   Mark Abraham
      • [gmx-users] precision of input gro file   Yu Ogawa
      • [gmx-users] precision of input gro file   Mark Abraham
      • [gmx-users] precision of input gro file   Yu Ogawa
• [gmx-users] General questions about topology building   Marko Sever
• [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   jay patil
  • [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   Christopher Neale
    • [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   jay patil
• [gmx-users] -bash: ngmx: command not found   Karchevskaya, Anastasia
  • [gmx-users] -bash: ngmx: command not found   Mark Abraham
• [gmx-users] Error when performing MD with heavy atoms frozen   Kai Hu
  • [gmx-users] Error when performing MD with heavy atoms frozen   Justin Lemkul
    • [gmx-users] Error when performing MD with heavy atoms frozen   Kai Hu
      • [gmx-users] Error when performing MD with heavy atoms frozen   Justin Lemkul
      • [gmx-users] Error when performing MD with heavy atoms frozen   Kai Hu
      • [gmx-users] Error when performing MD with heavy atoms frozen   Justin Lemkul
• [gmx-users] Space between the columns in the topology file of Gromacs   lan hoa Trinh
  • [gmx-users] Space between the columns in the topology file of Gromacs   Mark Abraham
    • [gmx-users] Space between the columns in the topology file of Gromacs   lan hoa Trinh
• [gmx-users] Vmd error   RAHUL SURESH
  • [gmx-users] Vmd error   Emran Heshmati
  • [gmx-users] Vmd error   Justin Lemkul
• [gmx-users] POTENTIAL ENERGY SURFACE SCAN   Neha Gupta
  • [gmx-users] POTENTIAL ENERGY SURFACE SCAN   Mark Abraham
    • [gmx-users] POTENTIAL ENERGY SURFACE SCAN   Neha Gupta
      • [gmx-users] POTENTIAL ENERGY SURFACE SCAN   Justin Lemkul
• [gmx-users] Vmd error   Quyen V. Vu
  • [gmx-users] Vmd error   Justin Lemkul
• [gmx-users] genion -conc give the wrong number of multi-valent counter ion   Quyen V. Vu
  • [gmx-users] genion -conc give the wrong number of multi-valent counter ion   Justin Lemkul
    • [gmx-users] genion -conc give the wrong number of multi-valent counter ion   Mark Abraham
• [gmx-users] Vmd error   Nikhil Maroli
• [gmx-users] (no subject)   Shivangi Agarwal
  • [gmx-users] (no subject)   Justin Lemkul
    • [gmx-users] (no subject)   Shivangi Agarwal
      • [gmx-users] (no subject)   Mark Abraham
      • [gmx-users] (no subject)   Emran Heshmati
  • [gmx-users] (no subject)   Emran Heshmati
• [gmx-users] Insert Gold nanoparticles in a simulation box   Sheikh Imamul Hossain
  • [gmx-users] Insert Gold nanoparticles in a simulation box   Dallas Warren
• [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   jay patil
• [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   jay patil
• [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   jay patil
• [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   jay patil
  • [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.   Justin Lemkul
• [gmx-users] System reaches ~124K after simulated annealing upto 300K   Apramita Chand
  • [gmx-users] System reaches ~124K after simulated annealing upto 300K   Justin Lemkul
• [gmx-users] Protein-ligand binding Cut-offs   Pandya, Akash
  • [gmx-users] Protein-ligand binding Cut-offs   Mark Abraham
    • [gmx-users] Protein-ligand binding Cut-offs   Pandya, Akash
      • [gmx-users] Protein-ligand binding Cut-offs   Mark Abraham
      • [gmx-users] Protein-ligand binding Cut-offs   Sergio Manzetti
    • [gmx-users] Protein-ligand binding Cut-offs   Pandya, Akash
      • [gmx-users] Protein-ligand binding Cut-offs   Mark Abraham
      • [gmx-users] Protein-ligand binding Cut-offs   Pandya, Akash
      • [gmx-users] Protein-ligand binding Cut-offs   Mark Abraham
      • [gmx-users] Protein-ligand binding Cut-offs   Pandya, Akash
      • [gmx-users] Protein-ligand binding Cut-offs   Mark Abraham
      • [gmx-users] Protein-ligand binding Cut-offs   Pandya, Akash
      • [gmx-users] Protein-ligand binding Cut-offs   Mark Abraham
      • [gmx-users] Protein-ligand binding Cut-offs   Pandya, Akash
• [gmx-users] amino acid topology   suniba shuaib
  • [gmx-users] amino acid topology   Justin Lemkul
• [gmx-users] Gromacs on GPU   Mohsen Ramezanpour
  • [gmx-users] Gromacs on GPU   Justin Lemkul
    • [gmx-users] Gromacs on GPU   Mohsen Ramezanpour
      • [gmx-users] Gromacs on GPU   Téletchéa Stéphane
      • [gmx-users] Gromacs on GPU   Mohsen Ramezanpour
      • [gmx-users] Gromacs on GPU   Justin Lemkul
• [gmx-users] Looking for longer running, publicly avail use cases   Maureen Chew
• [gmx-users] Dihedral angle parameters in Gromacs and Amber   lan hoa Trinh
  • [gmx-users] Dihedral angle parameters in Gromacs and Amber   Mark Abraham
• [gmx-users] How to parameterize the volume occupied by a protein?   Jose Borreguero
  • [gmx-users] How to parameterize the volume occupied by a protein?   Mark Abraham
    • [gmx-users] How to parameterize the volume occupied by a protein?   Jose Borreguero
• [gmx-users] System reaches ~124K after simulated annealing upto 300K (Justin Lemkul)   Apramita Chand
  • [gmx-users] System reaches ~124K after simulated annealing upto 300K (Justin Lemkul)   Justin Lemkul
• [gmx-users] How to create parameters for polyethyleneglycol (PEG) 6000 in a gromacs MD simulation   Sajeewa Pemasinghe
  • [gmx-users] How to create parameters for polyethyleneglycol (PEG) 6000 in a gromacs MD simulation   Justin Lemkul
• [gmx-users] using groups in index for gmx select   Nikhil Maroli
• [gmx-users] FLUCTUATION IN DISTANCE   Neha Gupta
  • [gmx-users] FLUCTUATION IN DISTANCE   Justin Lemkul
• [gmx-users] error in phosphoserine simulation during MD   marzieh dehghan
  • [gmx-users] error in phosphoserine simulation during MD   Justin Lemkul
• [gmx-users] CompEL bulk offset parameter unavailable in gromacs 5.1.4?   Vries, de, H.W.
  • [gmx-users] CompEL bulk offset parameter unavailable in gromacs 5.1.4?   Kutzner, Carsten
• [gmx-users] error in phosphoserine simulation during MD   marzieh dehghan
  • [gmx-users] error in phosphoserine simulation during MD   Justin Lemkul
• [gmx-users] error in phosphoserine simulation during MD   marzieh dehghan
  • [gmx-users] error in phosphoserine simulation during MD   Mark Abraham
• [gmx-users] hydrogen bond analysis   Md. Imrul Reza Shishir
  • [gmx-users] hydrogen bond analysis   João Henriques
    • [gmx-users] hydrogen bond analysis   Justin Lemkul
• [gmx-users] Pulling in opposite directions   Saumyak Mukherjee
• [gmx-users] distance restraint in gromacs md run   Simon Kit Sang Chu
  • [gmx-users] distance restraint in gromacs md run   Justin Lemkul
    • [gmx-users] distance restraint in gromacs md run   Simon Kit Sang Chu
      • [gmx-users] distance restraint in gromacs md run   Mark Abraham
• [gmx-users] Temperature control in fix gcmc with fix rigid/nvt/small   Youzhi Hao
  • [gmx-users] Temperature control in fix gcmc with fix rigid/nvt/small   Alex
• [gmx-users] Coulomb values   Merril Mathew
  • [gmx-users] Coulomb values   Justin Lemkul
• [gmx-users] Pull in a channel   François-Régis Chalaoux
  • [gmx-users] Pull in a channel   François-Régis Chalaoux
• [gmx-users] 5' phosphate of RNA   Mohammad fat habadi
  • [gmx-users] 5' phosphate of RNA   Justin Lemkul
• [gmx-users] xx inconsistent shift check your topology   Diez Fernandez, Amanda
• [gmx-users] phosphate atoms on 5' Of RNA   mohammad fathabadi
• [gmx-users] Temperature control in fix gcmc with fix rigid/nvt/small   Youzhi Hao
• [gmx-users] hydrogen bond analysis   Quyen V. Vu
• [gmx-users] Computing work from pulling simulations   Lutz Maibaum
  • [gmx-users] Computing work from pulling simulations   Leandro Bortot
    • [gmx-users] Computing work from pulling simulations   Lutz Maibaum
• [gmx-users] MD run error   Mishelle Oña
  • [gmx-users] MD run error   Mark Abraham
• [gmx-users] a problem about ewald geometry=3dc   Ali Shomali
• [gmx-users] a problem about ewald geometry=3dc   Ali Shomali
• [gmx-users] a problem about ewald geometry=3dc   Ali Shomali
  • [gmx-users] Fwd: a problem about ewald geometry=3dc   Ali Shomali
  • [gmx-users] a problem about ewald geometry=3dc   Philip Loche
    • [gmx-users] a problem about ewald geometry=3dc   Ali Shomali
      • [gmx-users] a problem about ewald geometry=3dc   Philip Loche
• [gmx-users] AVX related compiler error during build with P100 RHEL7   Guyen Gn
  • [gmx-users] AVX related compiler error during build with P100 RHEL7   Mark Abraham
• [gmx-users] Unable to generate umbrella histogram and PMF curve   Norfarisha Mohd Fadil
  • [gmx-users] Unable to generate umbrella histogram and PMF curve   Justin Lemkul
• [gmx-users] RMSD output from gmx confrms differs from gmx rms?   Susan Khor
• [gmx-users] Re : Unable to generate umbrella histogram and PMF curve   Norfarisha Mohd Fadil
  • [gmx-users] Re : Unable to generate umbrella histogram and PMF curve   Justin Lemkul
• [gmx-users] Regarding Creating a molecule and fitting it to CHARMM forcefield   Dilip H N
  • [gmx-users] Regarding Creating a molecule and fitting it to CHARMM forcefield   Mark Abraham
• [gmx-users] Topology generation of molecules   Abid Channa
  • [gmx-users] Topology generation of molecules   Justin Lemkul
    • [gmx-users] Topology generation of molecules   Smith, Micholas D.
• [gmx-users] (no subject)   Shivangi Agarwal
  • [gmx-users] (no subject)   Mark Abraham
    • [gmx-users] (no subject)   Shivangi Agarwal
      • [gmx-users] (no subject)   Mark Abraham
      • [gmx-users] (no subject)   Shivangi Agarwal
• [gmx-users] Adding multiple different ligands with acpype   Vytautas Rakeviius
  • [gmx-users] Adding multiple different ligands with acpype   Justin Lemkul
• [gmx-users] how to get omega angles for a trajectory?   Seera Suryanarayana
  • [gmx-users] how to get omega angles for a trajectory?   Mark Abraham
• [gmx-users] Difference between Err. Est. And RMSD   jay patil
  • [gmx-users] Difference between Err. Est. And RMSD   João Henriques
  • [gmx-users] Difference between Err. Est. And RMSD   Justin Lemkul
    • [gmx-users] Difference between Err. Est. And RMSD   jay patil
• [gmx-users] Error running GMX 5.14   Sergio Manzetti
  • [gmx-users] Error running mdrun em with Sodium ions in GMX 5.14   Sergio Manzetti
    • [gmx-users] Error running mdrun em with Sodium ions in GMX 5.14   Justin Lemkul
  • [gmx-users] Error running GMX 5.14   Smith, Micholas D.
    • [gmx-users] Error running GMX 5.14   Sergio Manzetti
      • [gmx-users] Error running GMX 5.14   Justin Lemkul
      • [gmx-users] Error running GMX 5.14   Sergio Manzetti
      • [gmx-users] Error running GMX 5.14   Justin Lemkul
      • [gmx-users] Error running GMX 5.14   Mark Abraham
      • [gmx-users] Error running GMX 5.14   Sergio Manzetti
      • [gmx-users] Error running GMX 5.14   Justin Lemkul
      • [gmx-users] Error running GMX 5.14   Sergio Manzetti
      • [gmx-users] Error running GMX 5.14   Justin Lemkul
      • [gmx-users] Error running GMX 5.14   Sergio Manzetti
      • [gmx-users] Error running GMX 5.14   Sergio Manzetti
      • [gmx-users] Error running GMX 5.14   Justin Lemkul
      • [gmx-users] Error running GMX 5.14   Sergio Manzetti
      • [gmx-users] Error running GMX 5.14   Justin Lemkul
      • [gmx-users] Error running GMX 5.14   Sergio Manzetti
      • [gmx-users] Error running GMX 5.14   Mark Abraham
      • [gmx-users] Error running GMX 5.14   Sergio Manzetti
    • [gmx-users] Error running GMX 5.14   Sergio Manzetti
• [gmx-users] GROMACS and SIMtoEXP   Sanim Rahman
  • [gmx-users] GROMACS and SIMtoEXP   David van der Spoel
    • [gmx-users] GROMACS and SIMtoEXP   Sanim Rahman
• [gmx-users] How to perform final MD simulation after extending a NPT simulation   Adarsh V. K.
  • [gmx-users] How to perform final MD simulation after extending a NPT simulation   Mark Abraham
• [gmx-users] (no subject)   Shivangi Agarwal
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] Regarding the charge of the atom in the .rtp file   Dilip H N
  • [gmx-users] Regarding the charge of the atom in the .rtp file   Mark Abraham
    • [gmx-users] Regarding the charge of the atom in the .rtp file   Dilip H N
      • [gmx-users] Regarding the charge of the atom in the .rtp file   Mark Abraham
      • [gmx-users] Regarding the charge of the atom in the .rtp file   Dilip H N
      • [gmx-users] Regarding the charge of the atom in the .rtp file   Justin Lemkul
• [gmx-users] Slow MDRUN performance   Syed Azeem
  • [gmx-users] Slow MDRUN performance   Mark Abraham
• [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates   Diez Fernandez, Amanda
  • [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates   Justin Lemkul
• [gmx-users] Slow MDRUN performance   Syed Azeem
  • [gmx-users] Slow MDRUN performance   Mark Abraham
• [gmx-users] (no subject)   Shivangi Agarwal
  • [gmx-users] (no subject)   Mark Abraham
    • [gmx-users] (no subject)   Shivangi Agarwal
      • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   gozde ergin
  • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   Mark Abraham
    • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   gozde ergin
      • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   Justin Lemkul
      • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   gozde ergin
      • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   Justin Lemkul
      • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   gozde ergin
      • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   Justin Lemkul
      • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   Mark Abraham
      • [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS   gozde ergin
• [gmx-users] Genion   Sergio Manzetti
  • [gmx-users] Genion   Justin Lemkul
    • [gmx-users] Genion   Sergio Manzetti
      • [gmx-users] Genion   Justin Lemkul
      • [gmx-users] Genion   Sergio Manzetti
      • [gmx-users] Genion   Sergio Manzetti
      • [gmx-users] Genion   Justin Lemkul
      • [gmx-users] Genion   Sergio Manzetti
      • [gmx-users] Genion   Justin Lemkul
      • [gmx-users] Genion   Sergio Manzetti
      • [gmx-users] Genion   Justin Lemkul
      • [gmx-users] Genion   Sergio Manzetti
      • [gmx-users] Genion   Mark Abraham
      • [gmx-users] Genion   Sergio Manzetti
• [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top   Jose Borreguero
  • [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top   Justin Lemkul
    • [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top   Jose Borreguero
      • [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top   Justin Lemkul
      • [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top   Jose Borreguero
• [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates   Diez Fernandez, Amanda
  • [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates   Mark Abraham
• [gmx-users] Pulling inside a channel to calculate the PMF   François-Régis Chalaoux
  • [gmx-users] Pulling inside a channel to calculate the PMF   Alex
    • [gmx-users] Pulling inside a channel to calculate the PMF   François-Régis Chalaoux
      • [gmx-users] Pulling inside a channel to calculate the PMF   Alex
      • [gmx-users] Pulling inside a channel to calculate the PMF   François-Régis Chalaoux
• [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates   Diez Fernandez, Amanda
  • [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates   Mark Abraham
• [gmx-users] positive potential energy   Emran Heshmati
  • [gmx-users] positive potential energy   Mark Abraham
• [gmx-users] Simulation of Carbon nanotube   Nikhil Maroli
  • [gmx-users] Simulation of Carbon nanotube   Justin Lemkul
• [gmx-users] Simulation of Carbon nanotube   Nikhil Maroli
  • [gmx-users] Simulation of Carbon nanotube   Justin Lemkul
• [gmx-users] MDP for DNA with ions   Sergio Manzetti
  • [gmx-users] MDP for DNA with ions   Justin Lemkul
    • [gmx-users] MDP for DNA with ions   Sergio Manzetti
      • [gmx-users] MDP for DNA with ions   Justin Lemkul
      • [gmx-users] MDP for DNA with ions   Sergio Manzetti
      • [gmx-users] MDP for DNA with ions   Sergio Manzetti
      • [gmx-users] MDP for DNA with ions   Justin Lemkul
• [gmx-users] Domain decomposition   Sergio Manzetti
  • [gmx-users] Domain decomposition   Justin Lemkul
    • [gmx-users] Domain decomposition   Sergio Manzetti
      • [gmx-users] Domain decomposition   Justin Lemkul
      • [gmx-users] Domain decomposition   Sergio Manzetti
• [gmx-users] Plotting Density Over Time?   Sanim Rahman
  • [gmx-users] Plotting Density Over Time?   Justin Lemkul
• [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates   Diez Fernandez, Amanda
  • [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates   Mark Abraham
• [gmx-users] How to get the correct reference frame to run the rmsf?   ZHANG Cheng
  • [gmx-users] How to get the correct reference frame to run the rmsf?   Justin Lemkul
• [gmx-users] System shrinkage during vacuum simulation   Sanim Rahman
  • [gmx-users] System shrinkage during vacuum simulation   David van der Spoel
    • [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults   Qing Lv
      • [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults   Qing Lv
      • [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults   Mark Abraham
      • [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults   Qing Lv
    • [gmx-users] 5-letter atom names in topology files   Qing Lv
      • [gmx-users] 5-letter atom names in topology files   Mark Abraham
      • [gmx-users] 5-letter atom names in topology files   Qing Lv
      • [gmx-users] 5-letter atom names in topology files   Qing Lv
      • [gmx-users] 5-letter atom names in topology files   Fitsiou, Eleni
      • [gmx-users] 5-letter atom names in topology files   Qing Lv
      • [gmx-users] 5-letter atom names in topology files   Justin Lemkul
      • [gmx-users] 5-letter atom names in topology files   Qing Lv
• [gmx-users] Constraint vs. Umbrella in Pull COM   Angela Marcela Murcia Rios
  • [gmx-users] Constraint vs. Umbrella in Pull COM   Alex
    • [gmx-users] Constraint vs. Umbrella in Pull COM   Angela Marcela Murcia Rios
• [gmx-users] g_rdf and g_select for number of res with COM within distance to surface   Patrick Charchar
• [gmx-users] Regarding creating a itp for molecule from CGenFF   Dilip H N
  • [gmx-users] Regarding creating a itp for molecule from CGenFF   Justin Lemkul
• [gmx-users] Which method for choosing concentration is more appropriate   Apramita Chand
• [gmx-users] Gigantic boxes   Sergio Manzetti
  • [gmx-users] Gigantic boxes   Justin Lemkul
    • [gmx-users] Gigantic boxes   Sergio Manzetti
• [gmx-users] Box size and Force field   Sergio Manzetti
• [gmx-users] Scaling GROMACS   Sergio Manzetti
  • [gmx-users] Scaling GROMACS   Justin Lemkul
  • [gmx-users] Scaling GROMACS   Mark Abraham
• [gmx-users] CG MD   Alex Mathew
  • [gmx-users] CG MD   Justin Lemkul
• [gmx-users] Legacy Test Failure with GMX 5.1.4   Daniel Kozuch
• [gmx-users] CGMD with cut-off Verlet?   Alex Mathew
  • [gmx-users] CGMD with cut-off Verlet?   Justin Lemkul
    • [gmx-users] CGMD with cut-off Verlet?   Mark Abraham
      • [gmx-users] CGMD with cut-off Verlet?   Peter Kroon
• [gmx-users] Exchange temperature instead of exchange coordinate in replica exchange molecular dynamics?   lan hoa Trinh
• [gmx-users] adding new ion within the oplsaa force field   Jose Borreguero
  • [gmx-users] adding new ion within the oplsaa force field   Smith, Micholas D.
  • [gmx-users] adding new ion within the oplsaa force field   Justin Lemkul
    • [gmx-users] adding new ion within the oplsaa force field   Jose Borreguero
• [gmx-users] Lincs constraints failure   Qinghua Liao
  • [gmx-users] Lincs constraints failure   Mark Abraham
    • [gmx-users] Lincs constraints failure   Qinghua Liao
      • [gmx-users] Lincs constraints failure   Mark Abraham
• [gmx-users] difference in potential energy   Emran Heshmati
• [gmx-users] difference in kinetic energy   Emran Heshmati
  • [gmx-users] difference in kinetic energy   Mark Abraham
• [gmx-users] an error related to Gromacs version   Mahboobeh Eslami
• [gmx-users] an error related to Gromacs version   ABEL Stephane
• [gmx-users] MD simulation at different pH   Anand Balupuri
  • [gmx-users] MD simulation at different pH   João Henriques
    • [gmx-users] MD simulation at different pH   Anand Balupuri
• [gmx-users] Spherical Water Droplet   Shraddha Parate
  • [gmx-users] Spherical Water Droplet   Alex
• [gmx-users] velocity profile in nanochannel flows   NOKK SIEMPRE
• [gmx-users] NPT error   ‪Mohammad Roostaie‬ ‪
• [gmx-users] Regarding conversion of charmm ff to gromacs by cgenff_charmm2gmx.py script   Dilip H N
  • [gmx-users] Regarding conversion of charmm ff to gromacs by cgenff_charmm2gmx.py script   Mark Abraham
• [gmx-users] dssp installation using cygwin   Neha Gupta
  • [gmx-users] dssp installation using cygwin   Mark Abraham
• [gmx-users] Regarding conversion of charmm ff to gromacs by cgenff_charmm2gmx.py script   Nikhil Maroli
• [gmx-users] Fwd: Relative free energy perturbation   Davide Bonanni
  • [gmx-users] Fwd: Relative free energy perturbation   Hannes Loeffler
• [gmx-users] How to convert AMBER trajectory to Gromacs trajectory   Saikat Pal
• [gmx-users] negative reaction coordinate during pulling   edesantis
• [gmx-users] CG MD   Alex Mathew
  • [gmx-users] CG MD   Peter Kroon
• [gmx-users] Regarding change in residue name during conversion from pdb 2 gro file   Dilip H N
  • [gmx-users] Regarding change in residue name during conversion from pdb 2 gro file   Mark Abraham
• [gmx-users] gmx distance   Pandya, Akash
• [gmx-users] How i can use amber heme ff in gromacs   Rana Rehan Khalid
• [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Rana Rehan Khalid
  • [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.   Mark Abraham
• [gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?   Apramita Chand
  • [gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?   Mark Abraham
• [gmx-users] Simulations stop running after reaching specific time step   Shobha Sharma
  • [gmx-users] Simulations stop running after reaching specific time step   Vytautas Rakeviius
  • [gmx-users] Simulations stop running after reaching specific time step   Mark Abraham
• [gmx-users] DNA splitting in simulations   Sergio Manzetti
  • [gmx-users] DNA splitting in simulations   João Henriques
    • [gmx-users] DNA splitting in simulations   Sergio Manzetti
      • [gmx-users] DNA splitting in simulations   Justin Lemkul
      • [gmx-users] DNA splitting in simulations   Sergio Manzetti
      • [gmx-users] DNA splitting in simulations   Justin Lemkul
• [gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?   Nikhil Maroli
• [gmx-users] CGMD with cut-off Verlet? production run stage   Alex Mathew
  • [gmx-users] CGMD with cut-off Verlet? production run stage   Mark Abraham
    • [gmx-users] CGMD with cut-off Verlet? production run stage   Peter Kroon
• [gmx-users] Difference between semi isotropic coupling and surface tension option   Ali Shomali
• [gmx-users] Simulation ended prematurely, no performance report will be written- Minimization   Alex Mathew
  • [gmx-users] Simulation ended prematurely, no performance report will be written- Minimization   Peter Kroon
• [gmx-users] Number of Contacts   Sundari chaudhary
  • [gmx-users] Number of Contacts   Dallas Warren
    • [gmx-users] Number of Contacts   Sundari
• [gmx-users] gmx spatial   Valerio Ferrario
  • [gmx-users] gmx spatial   Dallas Warren
    • [gmx-users] gmx spatial   Valerio Ferrario
• [gmx-users] adding a custom residue with an itp file   Jose Borreguero
  • [gmx-users] adding a custom residue with an itp file   Justin Lemkul
    • [gmx-users] adding a custom residue with an itp file   Jose Borreguero
• [gmx-users] By using the Gromacs to simulate Raman spectrum   lu lu
  • [gmx-users] By using the Gromacs to simulate Raman spectrum   Alex
• [gmx-users] Atom types comparison between CGenFF and Charm36FF   Mohsen Ramezanpour
  • [gmx-users] Atom types comparison between CGenFF and Charm36FF   Justin Lemkul
    • [gmx-users] Atom types comparison between CGenFF and Charm36FF   Mohsen Ramezanpour
      • [gmx-users] Atom types comparison between CGenFF and Charm36FF   Justin Lemkul
      • [gmx-users] Atom types comparison between CGenFF and Charm36FF   Mohsen Ramezanpour
• [gmx-users] (no subject)   Shivangi Agarwal
  • [gmx-users] (no subject)   Shivangi Agarwal
  • [gmx-users] (no subject)   Justin Lemkul
• [gmx-users] use INTERFACE Force Field   Мижээ Батсайхан
  • [gmx-users] use INTERFACE Force Field   Vytautas Rakeviius
    • [gmx-users] use INTERFACE Force Field   João Henriques
      • [gmx-users] use INTERFACE Force Field   João Henriques
• [gmx-users] Pullin dhiedral angle version 2016   Luca Retattino
• [gmx-users] Pram file to gromac converter   Rana Rehan Khalid
• [gmx-users] gmx wham problem   edesantis
  • [gmx-users] gmx wham problem   Thompson, Matthew White
• [gmx-users] Deform a liquid   nishi kashyap
• [gmx-users] Anybody using Silica InterfaceFF on Gromacs?   Diez Fernandez, Amanda
  • [gmx-users] Anybody using Silica InterfaceFF on Gromacs?   Alex
    • [gmx-users] Anybody using Silica InterfaceFF on Gromacs?   David van der Spoel
      • [gmx-users] Anybody using Silica InterfaceFF on Gromacs?   Alex
• [gmx-users] how we can use Amber ff that are frcmod.hem not present in gromacs   Rana Rehan Khalid
• [gmx-users] NVT.gro is not genetared   Sithara Perera
• [gmx-users] NVT.gro is not genetared   Nikhil Maroli
  • [gmx-users] NVT.gro is not genetared   Sithara Perera
• [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep   Sudip Das
  • [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep   Peter Kroon
    • [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep   Peter Kroon
• [gmx-users] NPT error   Mohammad Roostaie
• [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 181   Diez Fernandez, Amanda
• [gmx-users] Invalid angle type 0   Zuzana Benkova
  • [gmx-users] Invalid angle type 0   Justin Lemkul
• [gmx-users] In-vacuo minimization of peptide   Apramita Chand
  • [gmx-users] In-vacuo minimization of peptide   Justin Lemkul
• [gmx-users] Interpretation of MSD   Pandya, Akash
  • [gmx-users] Interpretation of MSD   Gaurav Goel
• [gmx-users] NoPbc   Mostafa Javaheri
  • [gmx-users] NoPbc   Mark Abraham
• [gmx-users] Principale component analysis , experiment and MD comparison   Nawel Mele
  • [gmx-users] Principale component analysis , experiment and MD comparison   Justin Lemkul
• [gmx-users] RemvingDummyAtoms   Mostafa Javaheri
  • [gmx-users] RemvingDummyAtoms   Mark Abraham
• [gmx-users] Running MD jobs using slurm on multiple nodes   Thanh Le
  • [gmx-users] Running MD jobs using slurm on multiple nodes   Mark Abraham
• [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 186   Thanh Le
  • [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 186   Mark Abraham
• [gmx-users] tju.zxy at gamil.com   Sofia Zhao
• [gmx-users] NVT.gro is not genetared   Sithara Perera
• [gmx-users] Nano-structures equilibration   Mohammad Roostaie
  • [gmx-users] Nano-structures equilibration   Alex
    • [gmx-users] Nano-structures equilibration   Mohammad Roostaie
      • [gmx-users] Nano-structures equilibration   Alex
• [gmx-users] dihedral angle calculation of glycosidic bond   Md. Imrul Reza Shishir
• [gmx-users] xtc with perl   gromacs query
  • [gmx-users] xtc with perl   Mark Abraham
    • [gmx-users] xtc with perl   gromacs query
• [gmx-users] reading topology by Gromacs   Mohsen Ramezanpour
• [gmx-users] Regarding grid spacing   Apramita Chand
• [gmx-users] topologies for Si-containing polymers   Alex

Last message date: Fri Jun 30 22:21:31 CEST 2017
Archived on: Fri Jun 30 22:21:31 CEST 2017

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