June 2017 Archives by date

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