July 2017 Archives by author

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Starting: Sat Jul 1 07:14:49 CEST 2017
Ending: Mon Jul 31 23:19:23 CEST 2017
Messages: 592

[gmx-users] Question on Umbrella Sampling with varied ionic strength. Yuanchao Liu (MSU)
[gmx-users] (no subject) qugm110 at 126.com
[gmx-users] replica exchange Mark Abraham
[gmx-users] MDrun -maxh option Mark Abraham
[gmx-users] MDrun -maxh option Mark Abraham
[gmx-users] Checkpoint files error Mark Abraham
[gmx-users] Issue with the PDB generated after topology Mark Abraham
[gmx-users] Anybody using Silica InterfaceFF on Gromacs? Mark Abraham
[gmx-users] Can not open file: run.trr Mark Abraham
[gmx-users] Can not open file: run.trr Mark Abraham
[gmx-users] Multiple output log. xtc .edr files generated using mpirun Mark Abraham
[gmx-users] Grid Spacing Mark Abraham
[gmx-users] Grid Spacing Mark Abraham
[gmx-users] Issue with the PDB generated after topology Mark Abraham
[gmx-users] Issue with the PDB generated after topology Mark Abraham
[gmx-users] Issue with the PDB generated after topology Mark Abraham
[gmx-users] (Not-) Changing protonation when using pdb2gmx Mark Abraham
[gmx-users] error in nvidia cuda installation Mark Abraham
[gmx-users] AVX related compiler error during build with P100 RHEL7 Mark Abraham
[gmx-users] re cant login to Gromacs User forum Mark Abraham
[gmx-users] re cant login to Gromacs User forum Mark Abraham
[gmx-users] re cant login to Gromacs User forum Mark Abraham
[gmx-users] Fatal error: Invalid character in digit-only string: '�' Mark Abraham
[gmx-users] Check for bad contacts and/or reduce the timestep Mark Abraham
[gmx-users] Fwd: Regarding getting the trajectories at certain time intervals Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] Invalid order for directive X Mark Abraham
[gmx-users] Regarding creating topology for molecule Mark Abraham
[gmx-users] Can't locate state.cpt for gmx mdrun Mark Abraham
[gmx-users] Invalid order for directive X Mark Abraham
[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules Mark Abraham
[gmx-users] Using an rtp file in an non standard directory Mark Abraham
[gmx-users] Using an rtp file in an non standard directory Mark Abraham
[gmx-users] Error of DNA topology Mark Abraham
[gmx-users] Help on MD performance, GPU has less load than CPU. Mark Abraham
[gmx-users] problem: gromacs run on gpu Mark Abraham
[gmx-users] Problem reading pdb files Mark Abraham
[gmx-users] Problem reading pdb files Mark Abraham
[gmx-users] DNa topology error. Mark Abraham
[gmx-users] output pdb reformatted Mark Abraham
[gmx-users] LINCS warning during constrained md Mark Abraham
[gmx-users] LINCS warning during constrained md Mark Abraham
[gmx-users] LINCS warning during constrained md Mark Abraham
[gmx-users] what is the difference between the 2016.x and the 5.x series? Mark Abraham
[gmx-users] what is the difference between the 2016.x and the 5.x series? Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] Help on MD performance, GPU has less load than CPU. Mark Abraham
[gmx-users] gmx select Mark Abraham
[gmx-users] gmx select Mark Abraham
[gmx-users] problem: gromacs run on gpu Mark Abraham
[gmx-users] Help on MD performance, GPU has less load than CPU. Mark Abraham
[gmx-users] Help on MD performance, GPU has less load than CPU. Mark Abraham
[gmx-users] xtc trajectory only Mark Abraham
[gmx-users] non-zero Coul-SR interaction between metal ion in the system with only one metal (GMX 5.0.7) Mark Abraham
[gmx-users] mdrun -rerun Mark Abraham
[gmx-users] mdrun -rerun Mark Abraham
[gmx-users] mdrun -rerun Mark Abraham
[gmx-users] mdrun -rerun Mark Abraham
[gmx-users] xtc trajectory only Mark Abraham
[gmx-users] Irregular relative entropy in free energy calculation Mark Abraham
[gmx-users] Using nose-Hoover thermostat with berendsen barostat Mark Abraham
[gmx-users] CHARMM force file error in gromacs Mark Abraham
[gmx-users] Did -ndec stop working in 2016 releases? Mark Abraham
[gmx-users] changing cutoffs with gmx tune_pme Mark Abraham
[gmx-users] Creating metal ion dummy models for MD simulations. Mark Abraham
[gmx-users] Molecular Simulation using Ionic liquid Mark Abraham
[gmx-users] Exclusion - determine neighboring atoms by atom indices or by bond connections? Mark Abraham
[gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function Mark Abraham
[gmx-users] Fatal error: Topology include file "drg.itp" not found Mark Abraham
[gmx-users] Non Standard Residue in Amber Mark Abraham
[gmx-users] G_MMPBSA Mark Abraham
[gmx-users] Simulation Restart Mark Abraham
[gmx-users] Simulation Restart Mark Abraham
[gmx-users] Simulation Restart Mark Abraham
[gmx-users] Simulation Restart Mark Abraham
[gmx-users] error message: Invalid transform ... Mark Abraham
[gmx-users] gmx complains of mismatch between index and trajectory file Mark Abraham
[gmx-users] gmx complains of mismatch between index and trajectory file Mark Abraham
[gmx-users] How to increase the volatile gpu-util Mark Abraham
[gmx-users] Using external force field with GROMACS Mark Abraham
[gmx-users] gmx check Mark Abraham
[gmx-users] gmx check Mark Abraham
[gmx-users] concatenate 2 trajectory files Mark Abraham
[gmx-users] error message: Invalid transform ... Mark Abraham
[gmx-users] How to increase the volatile gpu-util Mark Abraham
[gmx-users] How to increase the volatile gpu-util Mark Abraham
[gmx-users] problem on Gromacs 4.5.7 installation Mark Abraham
[gmx-users] compiling ambconv Mark Abraham
[gmx-users] problem on Gromacs 4.5.7 installation Mark Abraham
[gmx-users] problem on Gromacs 4.5.7 installation Mark Abraham
[gmx-users] Using external force field with GROMACS Mark Abraham
[gmx-users] Nucleic Acid in GROMOS54A7 Mark Abraham
[gmx-users] Nucleic Acid in GROMOS54A7 Mark Abraham
[gmx-users] multiple cpu for g_membed job? Mark Abraham
[gmx-users] Error in pdb2gmx Mark Abraham
[gmx-users] Error in pdb2gmx Mark Abraham
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Mark Abraham
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Mark Abraham
[gmx-users] Multiple output log. xtc .edr files generated using mpirun Abhishek Acharya
[gmx-users] Multiple output log. xtc .edr files generated using mpirun Abhishek Acharya
[gmx-users] Multiple output log. xtc .edr files generated using mpirun Abhishek Acharya
[gmx-users] Creating metal ion dummy models for MD simulations. Abhishek Acharya
[gmx-users] Creating metal ion dummy models for MD simulations. Abhishek Acharya
[gmx-users] Using external force field with GROMACS Souparno Adhikary
[gmx-users] Using external force field with GROMACS Souparno Adhikary
[gmx-users] (no subject) Souparno Adhikary
[gmx-users] Nucleic Acid in GROMOS54A7 Souparno Adhikary
[gmx-users] Nucleic Acid in GROMOS54A7 Souparno Adhikary
[gmx-users] (no subject) Shivangi Agarwal
[gmx-users] methylated HSP Emma Ahlstrand
[gmx-users] methylated HSP Emma Ahlstrand
[gmx-users] methylated HSP Emma Ahlstrand
[gmx-users] Creating Custom .rtp files Momin Ahmad
[gmx-users] Creating Custom .rtp files Momin Ahmad
[gmx-users] nitrogen itp file with virtual site Ali Ahmed
[gmx-users] nitrogen itp file with virtual site Ali Ahmed
[gmx-users] nitrogen itp file with virtual site Ali Ahmed
[gmx-users] nitrogen itp file with virtual site Ali Ahmed
[gmx-users] nitrogen itp file with virtual site Ali Ahmed
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Ali Ahmed
[gmx-users] MDrun -maxh option Akshay
[gmx-users] multiple cpu for g_membed job? Albert
[gmx-users] multiple cpu for g_membed job? Albert
[gmx-users] Nano-structures equilibration Alex
[gmx-users] Anybody using Silica InterfaceFF on Gromacs? Alex
[gmx-users] simulation at different temperature Alex
[gmx-users] simulation at different temperature Alex
[gmx-users] simulation at different temperature Alex
[gmx-users] dihedral angles in CNT Alex
[gmx-users] Modifying force field for graphene Alex
[gmx-users] output pdb reformatted Alex
[gmx-users] output pdb reformatted Alex
[gmx-users] Periodic Molecule's Free Energy Calculation Error Alex
[gmx-users] Periodic Molecule's Free Energy Calculation Error Alex
[gmx-users] problem: gromacs run on gpu Alex
[gmx-users] NPT problem Alex
[gmx-users] NPT problem Alex
[gmx-users] mdrun -rerun Alex
[gmx-users] mdrun -rerun Alex
[gmx-users] mdrun -rerun Alex
[gmx-users] mdrun -rerun Alex
[gmx-users] mdrun -rerun Alex
[gmx-users] mdrun -rerun Alex
[gmx-users] Periodic Molecule's Free Energy Calculation Error Alex
[gmx-users] NPT problem Alex
[gmx-users] NPT problem Alex
[gmx-users] Damping for pulled group Alex
[gmx-users] Damping for pulled group Alex
[gmx-users] Damping for pulled group Alex
[gmx-users] Molecular Simulation using Ionic liquid Alex
[gmx-users] units of gmx wham output Irem Altan
[gmx-users] Issue with the PDB generated after topology Khadija Amine
[gmx-users] Issue with the PDB generated after topology Khadija Amine
[gmx-users] Issue with the PDB generated after topology Khadija Amine
[gmx-users] Issue with the PDB generated after topology Khadija Amine
[gmx-users] Issue with the PDB generated after topology Khadija Amine
[gmx-users] Ligand and ion topology Khadija Amine
[gmx-users] Ligand and ion topology Khadija Amine
[gmx-users] Invalid order for directive X Khadija Amine
[gmx-users] Invalid order for directive X Khadija Amine
[gmx-users] Invalid order for directive X Khadija Amine
[gmx-users] Add missing residues Khadija Amine
[gmx-users] Gmx 2016.3 compilation error on PHI Jones de Andrade
[gmx-users] Molecular Simulation using Ionic liquid Antonio Baptista
[gmx-users] Regarding terminal residue parameters (Capping) Sagar Barale
[gmx-users] dihedral angles in CNT Zuzana Benkova
[gmx-users] Try NVIDIA's GPU-Ready Applications Installation, Running, Benchmark "Recipe" for a quick on ramp to GROMACS on GPUs Mark Berger
[gmx-users] NEMD with sinusoidal pressure variation Aarushi Bhargava
[gmx-users] NEMD with sinusoidal pressure variation Aarushi Bhargava
[gmx-users] pulsed external pressure on protein Aarushi Bhargava
[gmx-users] Error in simulating graphene B S Bhushan
[gmx-users] Error in simulating graphene B S Bhushan
[gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 165 Davide Bonanni
[gmx-users] Fwd: Relative free energy perturbation Davide Bonanni
[gmx-users] Help on MD performance, GPU has less load than CPU. Davide Bonanni
[gmx-users] Crash in minimization that involves dummy atoms Davide Bonanni
[gmx-users] gmx bar Davide Bonanni
[gmx-users] what is the difference between the 2016.x and the 5.x series? Jose Borreguero
[gmx-users] what is the difference between the 2016.x and the 5.x series? Jose Borreguero
[gmx-users] changing cutoffs with gmx tune_pme Leandro Bortot
[gmx-users] Automake problem during installation 4.5.7 CHEN, Yu Wai [ABCT]
[gmx-users] Using an rtp file in an non standard directory Miguel Caro
[gmx-users] Computing free energy differences from the dH/dl values directly Miguel Caro
[gmx-users] Computing free energy differences from the dH/dl values directly Miguel Caro
[gmx-users] Checkpoint files error Apramita Chand
[gmx-users] Regarding grid spacing Apramita Chand
[gmx-users] Grid Spacing Apramita Chand
[gmx-users] Performance values Maureen Chew
[gmx-users] Performance values Maureen Chew
[gmx-users] Gromacs 5.0 - Solvent Accessible Surface Area (sasa) separate Hydrophobic and Hydrophilic components Nuria Codina
[gmx-users] Solvent Accessible Surface Area (SASA): Separate Hydrophobic and Hydrophilic components Nuria Codina
[gmx-users] problem on Gromacs 4.5.7 installation Rahma Dahmani
[gmx-users] problem on Gromacs 4.5.7 installation Rahma Dahmani
[gmx-users] CHARMM force file error in gromacs Vikram Dalal
[gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep Sudip Das
[gmx-users] CG to AA backmapping: problem in using initram.sh script Sudip Das
[gmx-users] CG to AA backmapping: problem in using initram.sh script Sudip Das
[gmx-users] CG to AA backmapping: problem in using initram.sh script Sudip Das
[gmx-users] Best Force Field For Gases at High pressure Sam Dav
[gmx-users] ACCELERATE SIMULATION Aman Deep
[gmx-users] error in NVT run Aman Deep
[gmx-users] Non Standard Residue in Amber Souvik Dey
[gmx-users] Non Standard Residue in Amber Souvik Dey
[gmx-users] Error in pdb2gmx Souvik Dey
[gmx-users] Error in pdb2gmx Souvik Dey
[gmx-users] Anybody using Silica InterfaceFF on Gromacs? Diez Fernandez, Amanda
[gmx-users] Anybody using Silica InterfaceFF on Gromacs? Diez Fernandez, Amanda
[gmx-users] Error in Coarse Graining the atomistic trajectory Anurag Dobhal
[gmx-users] Fatal error: Invalid character in digit-only string: '�' Du, Yu
[gmx-users] Fatal error: Invalid character in digit-only string: '�' Du, Yu
[gmx-users] Concrete pull code explanation needed Du, Yu
[gmx-users] Concrete pull code explanation needed Du, Yu
[gmx-users] Concrete pull code explanation needed Du, Yu
[gmx-users] Accessible Surface Area (ASA) for each residue per frame Maximilian Ebert
[gmx-users] 'fudgeQQ' parameter in the topology file Sara Del Galdo
[gmx-users] 'fudgeQQ' parameter in the topology file Sara Del Galdo
[gmx-users] gmx_mpi mdrun with multidir and tabulated bond potentials Andrei Gasic
[gmx-users] AVX related compiler error during build with P100 RHEL7 Guyen Gn
[gmx-users] AVX related compiler error during build with P100 RHEL7 Guyen Gn
[gmx-users] AVX related compiler error during build with P100 RHEL7 Guyen Gn
[gmx-users] Regarding terminal residue parameters (Capping) Harry Mark Greenblatt
[gmx-users] ForceField for Zn Harry Mark Greenblatt
[gmx-users] Issue with the PDB generated after topology João Henriques
[gmx-users] 4-letter residues João Henriques
[gmx-users] 4-letter residues João Henriques
[gmx-users] (Not-) Changing protonation when using pdb2gmx Hermann, Johannes
[gmx-users] (Not-) Changing protonation when using pdb2gmx Hermann, Johannes
[gmx-users] Charge Mutation (State B) for Ions Hermann, Johannes
[gmx-users] Charge Mutation (State B) for Ions Hermann, Johannes
[gmx-users] Fatal error: Invalid character in digit-only string: '�' Hermann, Johannes
[gmx-users] Charge Mutation (State B) for Ions Hermann, Johannes
[gmx-users] error in NVT run Hermann, Johannes
[gmx-users] Box was shifted at least 10 times Sheikh Imamul Hossain
[gmx-users] Order parameter calculation Sheikh Imamul Hossain
[gmx-users] how could i question there? Sheikh Imamul Hossain
[gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs SOMNATH JAN
[gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs SOMNATH JAN
[gmx-users] Dummy atom vs Real atom Mostafa Javaheri
[gmx-users] (no subject) CLARK NICOLAS Joan
[gmx-users] How to analyze after extending a simulation? Adarsh V. K.
[gmx-users] How to analyze after extending a simulation? Adarsh V. K.
[gmx-users] Strange acceleration behaviour after continuation Kamps, M.
[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules Tasneem Kausar
[gmx-users] can i produce the NO force files for system Rana Rehan Khalid
[gmx-users] How to convert amber prep and param file to gromac topology file Rana Rehan Khalid
[gmx-users] energy minization mdp Mohammad Zahidul Hossain Khan
[gmx-users] energy minization mdp Mohammad Zahidul Hossain Khan
[gmx-users] ligand topology Mohammad Zahidul Hossain Khan
[gmx-users] error message: Invalid transform ... Clinton King
[gmx-users] error message: Invalid transform ... Clinton King
[gmx-users] About the QM/MM MD of Gromacs Clinton King
[gmx-users] Non-periodic COM Pulling Daniel Kozuch
[gmx-users] Non-periodic COM Pulling Daniel Kozuch
[gmx-users] Umbrella Sampling with Direction-Periodic Pulling Daniel Kozuch
[gmx-users] PCA two ensembles different atoms order Peter Kroon
[gmx-users] Fwd: PCA two ensembles different atoms order Peter Kroon
[gmx-users] CG to AA backmapping: problem in using initram.sh script Peter Kroon
[gmx-users] CG to AA backmapping: problem in using initram.sh script Peter Kroon
[gmx-users] about quality of CPUs with GPUS Kumar Meena, Santosh
[gmx-users] How to convert two domains of prtoein into two beads by Conarse-grained Molecular Dynamics (CG-MD)? Indu Kumari
[gmx-users] How to convert two domains of prtoein into two beads by Conarse-grained Molecular Dynamics (CG-MD)? Indu Kumari
[gmx-users] protein protein interaction: side chain contribution Justin Lemkul
[gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs Justin Lemkul
[gmx-users] Ligand and ion topology Justin Lemkul
[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI Justin Lemkul
[gmx-users] Automake problem during installation 4.5.7 Justin Lemkul
[gmx-users] methylated HSP Justin Lemkul
[gmx-users] Acetonitrile and isopropanol with CHARMM ff Justin Lemkul
[gmx-users] Flat-bottom spherical potential Justin Lemkul
[gmx-users] simulation at different temperature Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Acetonitrile with CHARMM ff Justin Lemkul
[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI Justin Lemkul
[gmx-users] Charge Mutation (State B) for Ions Justin Lemkul
[gmx-users] simulation at different temperature Justin Lemkul
[gmx-users] Acetonitrile with CHARMM ff Justin Lemkul
[gmx-users] Charge Mutation (State B) for Ions Justin Lemkul
[gmx-users] Doubt about Free Energy control Minimization Justin Lemkul
[gmx-users] Generating GROMACS input file from the GAMESS output file Justin Lemkul
[gmx-users] protein protein interaction: side chain contribution Justin Lemkul
[gmx-users] Acetonitrile with CHARMM ff Justin Lemkul
[gmx-users] Can't locate state.cpt for gmx mdrun Justin Lemkul
[gmx-users] Generating GROMACS input file from the GAMESS output file Justin Lemkul
[gmx-users] Acetonitrile using CHARMM ff Justin Lemkul
[gmx-users] ligan minimization in vacuo Justin Lemkul
[gmx-users] Concrete pull code explanation needed Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Justin Lemkul
[gmx-users] 5' phosphate of RNA Justin Lemkul
[gmx-users] Modifying force field for graphene Justin Lemkul
[gmx-users] RDF Justin Lemkul
[gmx-users] umbrella sampling Justin Lemkul
[gmx-users] umbrella sampling Justin Lemkul
[gmx-users] RDF Justin Lemkul
[gmx-users] DNA topology error Justin Lemkul
[gmx-users] output pdb reformatted Justin Lemkul
[gmx-users] umbrella sampling Justin Lemkul
[gmx-users] Concrete pull code explanation needed Justin Lemkul
[gmx-users] ACETONITRILE with CHARM ff Justin Lemkul
[gmx-users] Non-periodic COM Pulling Justin Lemkul
[gmx-users] Periodic Molecule's Free Energy Calculation Error Justin Lemkul
[gmx-users] gmx select Justin Lemkul
[gmx-users] Error in simulating graphene Justin Lemkul
[gmx-users] Acetonitrile with CHARMM ff Justin Lemkul
[gmx-users] 4-letter residues Justin Lemkul
[gmx-users] gmx select Justin Lemkul
[gmx-users] frozen ligand for free energy calculations Justin Lemkul
[gmx-users] Ramping down the restraint on molecules Justin Lemkul
[gmx-users] Equilibration Justin Lemkul
[gmx-users] frozen ligand for free energy calculations Justin Lemkul
[gmx-users] Non-periodic COM Pulling Justin Lemkul
[gmx-users] Concrete pull code explanation needed Justin Lemkul
[gmx-users] equilibration Justin Lemkul
[gmx-users] Regarding generating distance restraint Justin Lemkul
[gmx-users] Regarding precision in gromacs Justin Lemkul
[gmx-users] nitrogen itp file with virtual site Justin Lemkul
[gmx-users] NVT simulations for poylsaccharides in CHARMM36 Justin Lemkul
[gmx-users] nitrogen itp file with virtual site Justin Lemkul
[gmx-users] sd integrator and P-R barostat/ACETONITRILE with CHARMM ff Justin Lemkul
[gmx-users] nitrogen itp file with virtual site Justin Lemkul
[gmx-users] NVT simulations for poylsaccharides in CHARMM36 Justin Lemkul
[gmx-users] Equilibration of Lipid Bilayers created through charmm-gui Justin Lemkul
[gmx-users] nitrogen itp file with virtual site Justin Lemkul
[gmx-users] Regarding pdb2gmx and mdrun Justin Lemkul
[gmx-users] Using nose-Hoover thermostat with berendsen barostat Justin Lemkul
[gmx-users] Ethanol energies with CHARMM ff Justin Lemkul
[gmx-users] Damping for pulled group Justin Lemkul
[gmx-users] nitrogen itp file with virtual site Justin Lemkul
[gmx-users] Ethanol energies with CHARMM ff Justin Lemkul
[gmx-users] Drude force field Justin Lemkul
[gmx-users] protein -ligand complex dissociating during simulation Justin Lemkul
[gmx-users] Did -ndec stop working in 2016 releases? Justin Lemkul
[gmx-users] Doubt about edr file after normal mode analysis Justin Lemkul
[gmx-users] Dummy atom vs Real atom Justin Lemkul
[gmx-users] protein -ligand complex dissociating during simulation Justin Lemkul
[gmx-users] Regarding creating a box around the molecule and neutralization of charge before EM and MD Justin Lemkul
[gmx-users] energy minization mdp Justin Lemkul
[gmx-users] Question on force field Justin Lemkul
[gmx-users] Simulation of an acetylated peptide covalently bound to a protein Zixian Li
[gmx-users] Using external force field with GROMACS Qinghua Liao
[gmx-users] Fwd: Relative free energy perturbation Hannes Loeffler
[gmx-users] re cant login to Gromacs User forum Anna Lohning
[gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx Anna Lohning
[gmx-users] (no subject) Jivesh Madan
[gmx-users] NVT simulations for poylsaccharides in CHARMM36 Jivesh Madan
[gmx-users] NVT simulations for poylsaccharides in CHARMM36 Jivesh Madan
[gmx-users] ForceField for Zn Erik Marklund
[gmx-users] ForceField for Zn Erik Marklund
[gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function Erik Marklund
[gmx-users] Grid Spacing Nikhil Maroli
[gmx-users] Multiple output log. xtc .edr files generated using mpirun Nikhil Maroli
[gmx-users] Issue with the PDB generated after topology Nikhil Maroli
[gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 3 Nikhil Maroli
[gmx-users] error in nvidia cuda installation Nikhil Maroli
[gmx-users] problem: gromacs run on gpu Nikhil Maroli
[gmx-users] Regarding creating topology for molecule Nikhil Maroli
[gmx-users] Invalid order for directive X Nikhil Maroli
[gmx-users] Add missing residues Nikhil Maroli
[gmx-users] No procheck output for md starting structure. Nikhil Maroli
[gmx-users] Secondary structure analysis graph rescale Nikhil Maroli
[gmx-users] simulation at different temperature Alex Mathew
[gmx-users] simulation at different temperature Alex Mathew
[gmx-users] simulation at different temperature Alex Mathew
[gmx-users] PCA two ensembles different atoms order Nawel Mele
[gmx-users] PCA two ensembles different atoms order Nawel Mele
[gmx-users] PCA two ensembles different atoms order Nawel Mele
[gmx-users] Fwd: PCA two ensembles different atoms order Nawel Mele
[gmx-users] Fwd: PCA two ensembles different atoms order Nawel Mele
[gmx-users] Problem reading pdb files Nawel Mele
[gmx-users] Problem reading pdb files Nawel Mele
[gmx-users] How can I implement a radial potential field in GROMACS? Wes Michaels
[gmx-users] Walls and PME for long range electrostatics Alexander Miessen
[gmx-users] Did -ndec stop working in 2016 releases? Caro Miguel
[gmx-users] Did -ndec stop working in 2016 releases? Caro Miguel
[gmx-users] Did -ndec stop working in 2016 releases? Caro Miguel
[gmx-users] protein protein interaction: side chain contribution Tushar Ranjan Moharana
[gmx-users] protein protein interaction: side chain contribution Tushar Ranjan Moharana
[gmx-users] protein protein interaction: side chain contribution Tushar Ranjan Moharana
[gmx-users] umbrella sampling André Farias de Moura
[gmx-users] Regarding getting the trajectories at certain time intervals Dilip H N
[gmx-users] Fwd: Regarding getting the trajectories at certain time intervals Dilip H N
[gmx-users] Regarding creating topology for molecule Dilip H N
[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules Dilip H N
[gmx-users] Regarding precision in gromacs Dilip H N
[gmx-users] Regarding calculation of coordination number Dilip H N
[gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function Dilip H N
[gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function Dilip H N
[gmx-users] TIP4P/ice pdb file Christopher Neale
[gmx-users] TIP4P/ice pdb file Christopher Neale
[gmx-users] On the modeling of a shear flow Gleb Novikov
[gmx-users] Hyper-threading on multi-CPU xeon worstation Gleb Novikov
[gmx-users] dihedral restraint Yu Ogawa
[gmx-users] Regarding generating distance restraint Chinmai P
[gmx-users] RDF Saikat Pal
[gmx-users] RDF Pandya, Akash
[gmx-users] RDF Pandya, Akash
[gmx-users] gmx select Pandya, Akash
[gmx-users] gmx select Pandya, Akash
[gmx-users] gmx select Pandya, Akash
[gmx-users] gmx select Pandya, Akash
[gmx-users] RDF Values Pandya, Akash
[gmx-users] Number of Clusters during my simulation Pandya, Akash
[gmx-users] Flat-bottom spherical potential Shraddha Parate
[gmx-users] Drude force field Shraddha Parate
[gmx-users] ForceField for Zn Anjali Patel
[gmx-users] xtc trajectory only Atila Petrosian
[gmx-users] xtc trajectory only Atila Petrosian
[gmx-users] concatenate 2 trajectory files Atila Petrosian
[gmx-users] Scd or -Scd? Thomas Piggot
[gmx-users] Scd or -Scd? Thomas Piggot
[gmx-users] about quality of CPUs with GPUS Szilárd Páll
[gmx-users] Gromacs installation fails in CentOS 6.5 Szilárd Páll
[gmx-users] Gromacs installation fails in CentOS 6.5 Szilárd Páll
[gmx-users] problem: gromacs run on gpu Szilárd Páll
[gmx-users] Hardware for GROMACS Szilárd Páll
[gmx-users] Gromacs installation fails in CentOS 6.5 Szilárd Páll
[gmx-users] Gromacs installation fails in CentOS 6.5 Szilárd Páll
[gmx-users] problem: gromacs run on gpu Szilárd Páll
[gmx-users] what is the difference between the 2016.x and the 5.x series? Szilárd Páll
[gmx-users] Benchmarks v5.0 Szilárd Páll
[gmx-users] TIP4P/ice pdb file G R
[gmx-users] TIP4P/ice pdb file G R
[gmx-users] RDF Vidya R
[gmx-users] compiling ambconv Vidya R
[gmx-users] replica exchange Neda Rafiee
[gmx-users] error in nvidia cuda installation Neda Rafiee
[gmx-users] error in nvidia cuda installation Neda Rafiee
[gmx-users] error in nvidia cuda installation Neda Rafiee
[gmx-users] error in nvidia cuda installation Neda Rafiee
[gmx-users] error in nvidia cuda installation Neda Rafiee
[gmx-users] Doubt about Free Energy control Minimization Varvdekar Bhagyesh Rajendra
[gmx-users] Doubt about edr file after normal mode analysis Varvdekar Bhagyesh Rajendra
[gmx-users] Can not open file: run.trr Samith Rathnayake
[gmx-users] Can not open file: run.trr Samith Rathnayake
[gmx-users] User-defined Nonbonded Potentials and Cutoff Treatment Phillip Rauscher
[gmx-users] Gromacs installation fails in CentOS 6.5 Seyed Mostafa Razavi
[gmx-users] Gromacs installation fails in CentOS 6.5 Seyed Mostafa Razavi
[gmx-users] Gromacs installation fails in CentOS 6.5 Seyed Mostafa Razavi
[gmx-users] protein -ligand complex dissociating during simulation RAHUL SURESH
[gmx-users] protein -ligand complex dissociating during simulation RAHUL SURESH
[gmx-users] Creating Custom .rtp files RAHUL SURESH
[gmx-users] gmx complains of mismatch between index and trajectory file Jared Sagendorf
[gmx-users] Acetonitrile and isopropanol with CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] gromacs.org_gmx-users Digest, Acetonitrile with CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] Acetonitrile with CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] Acetonitrile with CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] Acetonitrile using CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] ACETONITRILE with CHARM ff Sonia Milena Aguilera Segura
[gmx-users] Acetonitrile with CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] sd integrator and P-R barostat/ACETONITRILE with CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] Ethanol energies with CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] Ethanol energies with CHARMM ff Sonia Milena Aguilera Segura
[gmx-users] Check for bad contacts and/or reduce the timestep Md. Imrul Reza Shishir
[gmx-users] Difference between semi isotropic coupling and surface tension option Ali Shomali
[gmx-users] Hardware for GROMACS Raman Preet Singh
[gmx-users] TIP3P WATER Srijan Singh
[gmx-users] 1st CfP: From Virtual Reality to Immersive Analytics in Bioinformatics (SD&A 2018) Björn Sommer
[gmx-users] Orientation restraints test case wanted. David van der Spoel
[gmx-users] g_clustsize question David van der Spoel
[gmx-users] NEMD with sinusoidal pressure variation David van der Spoel
[gmx-users] pulsed external pressure on protein David van der Spoel
[gmx-users] vdW and Coulombic forces David van der Spoel
[gmx-users] Using external force field with GROMACS David van der Spoel
[gmx-users] topology file with virtual site for an asymetric linear molecule ABEL Stephane
[gmx-users] topology servers versus ff ABEL Stephane
[gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx Peter Stern
[gmx-users] pdb2gmx Peter Stern
[gmx-users] Secondary structure analysis graph rescale SEB120010 Student
[gmx-users] Help on MD performance, GPU has less load than CPU. Téletchéa Stéphane
[gmx-users] Help on MD performance, GPU has less load than CPU. Téletchéa Stéphane
[gmx-users] Molecular Simulation using Ionic liquid Vidya Sundaram
[gmx-users] Number of Contacts Sundari
[gmx-users] Has omega -180 also in proteins? Seera Suryanarayana
[gmx-users] No procheck output for md starting structure. Seera Suryanarayana
[gmx-users] error in nvidia cuda installation Stephane TELETCHEA
[gmx-users] umbrella sampling Ben Tam
[gmx-users] umbrella sampling Ben Tam
[gmx-users] umbrella sampling Ben Tam
[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI Nidhin Thomas
[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI Nidhin Thomas
[gmx-users] Equilibration of Lipid Bilayers created through charmm-gui Nidhin Thomas
[gmx-users] Exclusion - determine neighboring atoms by atom indices or by bond connections? lan hoa Trinh
[gmx-users] ATOMTYPES directive lan hoa Trinh
[gmx-users] How to define (or modify) a new potential function in Gromacs? lan hoa Trinh
[gmx-users] Regarding pdb2gmx and mdrun S M Bargeen Turzo
[gmx-users] Regarding creating a box around the molecule and neutralization of charge before EM and MD S M Bargeen Turzo
[gmx-users] Regarding entropy of a protein-ligand complex S M Bargeen Turzo
[gmx-users] G_MMPBSA S M Bargeen Turzo
[gmx-users] error in nvidia cuda installation Stéphane Téletchéa
[gmx-users] Ramping down the restraint on molecules Lakshman Ji Verma
[gmx-users] Ramping down the restraint on molecules Lakshman Ji Verma
[gmx-users] protein -ligand complex dissociating during simulation Sneha Vishwanath
[gmx-users] protein -ligand complex dissociating during simulation Sneha Vishwanath
[gmx-users] protein -ligand complex dissociating during simulation Sneha Vishwanath
[gmx-users] Configuration of new HPC Cluster for GROMACS and NAMD Vogel, Alexander
[gmx-users] Has omega -180 also in proteins? András Ferenc WACHA
[gmx-users] gmx spatial Dallas Warren
[gmx-users] How to analyze after extending a simulation? Dallas Warren
[gmx-users] Best Force Field For Gases at High pressure Dallas Warren
[gmx-users] Regarding calculation of coordination number Dallas Warren
[gmx-users] Question on force field YanhuaOuyang
[gmx-users] Question on force field YanhuaOuyang
[gmx-users] frozen ligand for free energy calculations Ahmet Yildirim
[gmx-users] frozen ligand for free energy calculations Ahmet Yildirim
[gmx-users] Can't locate state.cpt for gmx mdrun Yonatan Zelnik
[gmx-users] Can't locate state.cpt for gmx mdrun Yonatan Zelnik
[gmx-users] Periodic Molecule's Free Energy Calculation Error Jason Zhu
[gmx-users] Periodic Molecule's Free Energy Calculation Error Jason Zhu
[gmx-users] Periodic Molecule's Free Energy Calculation Error Jason Zhu
[gmx-users] (no subject) Jason Zhu
[gmx-users] Periodic Molecule's Free Energy Calculation Error Jason Zhu
[gmx-users] Irregular relative entropy in free energy calculation Patrick armstrong
[gmx-users] Irregular relative entropy in free energy calculation Patrick armstrong
[gmx-users] gmx check Dawid das
[gmx-users] gmx check Dawid das
[gmx-users] gmx check Dawid das
[gmx-users] Calculate RMSD between snapshots of two trajectories Dawid das
[gmx-users] TIP4P-D Water itp file atanu das
[gmx-users] membrane simulation marzieh dehghan
[gmx-users] dihedral restraint gangotri dey
[gmx-users] protein -ligand complex dissociating during simulation gangotri dey
[gmx-users] gmx wham problem edesantis
[gmx-users] gmx wham problem edesantis
[gmx-users] LINCS warning during constrained md edesantis
[gmx-users] LINCS warning during constrained md edesantis
[gmx-users] LINCS warning during constrained md edesantis
[gmx-users] LINCS warning during constrained md edesantis
[gmx-users] pull COM "geometry = direction periodic" problem edesantis
[gmx-users] hole in the simulation box edesantis
[gmx-users] units of gmx wham output gozde ergin
[gmx-users] 5' phosphate of RNA mohammad fathabadi
[gmx-users] Scd or -Scd? m g
[gmx-users] how could i question there? faru honey
[gmx-users] Fatal error: Topology include file "drg.itp" not found faru honey
[gmx-users] RDF Values spss4 at iacs.res.in
[gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 3 amitabh jayaswal
[gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 24 amitabh jayaswal
[gmx-users] RDF Values saima kalsoom
[gmx-users] problem: gromacs run on gpu leila karami
[gmx-users] problem: gromacs run on gpu leila karami
[gmx-users] problem: gromacs run on gpu leila karami
[gmx-users] problem: gromacs run on gpu leila karami
[gmx-users] volatile gpu-util leila karami
[gmx-users] How to increase the volatile gpu-util leila karami
[gmx-users] How to increase the volatile gpu-util leila karami
[gmx-users] How to increase the volatile gpu-util leila karami
[gmx-users] Error of DNA topology maria khan
[gmx-users] DNa topology error. maria khan
[gmx-users] DNA topology error maria khan
[gmx-users] topology servers versus ff. maria khan
[gmx-users] PMF ligand membrane protein nahren manuel
[gmx-users] Simulation Restart mohamed mehana
[gmx-users] the sum of the two largest charge group radii is larger than rlist morpheus
[gmx-users] gmx select querry shivangi nangia
[gmx-users] Fwd: gmx select querry shivangi nangia
[gmx-users] vdW and Coulombic forces diana p
[gmx-users] Using nose-Hoover thermostat with berendsen barostat jay patil
[gmx-users] Using nose-Hoover thermostat with berendsen barostat jay patil
[gmx-users] Using nose-Hoover thermostat with berendsen barostat jay patil
[gmx-users] Using nose-Hoover thermostat with berendsen barostat jay patil
[gmx-users] Pull constrained Water molecule giving Lincs warning jay patil
[gmx-users] Methodology to determine permeability and diffusivity by constrained water molecule using umbrella constraint jay patil
[gmx-users] Simulation Restart jay patil
[gmx-users] Simulation Restart jay patil
[gmx-users] non-zero Coul-SR interaction between metal ion in the system with only one metal (GMX 5.0.7) qiaobf
[gmx-users] g_clustsize question antra saxena
[gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 125 suniba shuaib
[gmx-users] Benchmarks v5.0 jony.castagna at stfc.ac.uk
[gmx-users] Fw: EQUILIBRATION farial tavakoli
[gmx-users] Equilibration farial tavakoli
[gmx-users] Equilibration farial tavakoli
[gmx-users] Equilibration farial tavakoli
[gmx-users] Ligand topology farial tavakoli
[gmx-users] Extend the protein simulation farial tavakoli
[gmx-users] Hydroxyapatites parameter Мижээ Батсайхан
[gmx-users] mdmat calculation of heavy atoms of two side chains Мижээ Батсайхан
[gmx-users] gmx mdmat calculation of heavy atoms of two side chains Мижээ Батсайхан
[gmx-users] Nano-structures equilibration ‪Mohammad Roostaie‬ ‪
[gmx-users] Modifying force field for graphene ‪Mohammad Roostaie‬ ‪
[gmx-users] Modifying force field for graphene ‪Mohammad Roostaie‬ ‪
[gmx-users] NPT problem ‪Mohammad Roostaie‬ ‪
[gmx-users] NPT problem ‪Mohammad Roostaie‬ ‪
[gmx-users] NPT problem ‪Mohammad Roostaie‬ ‪
[gmx-users] EQUILIBRATION ‪farial tavakoli‬ ‪
[gmx-users] how to creat ligand topology to minimize in vacuo in the absence of the protein ‪farial tavakoli‬ ‪
[gmx-users] ligan minimization in vacuo ‪farial tavakoli‬ ‪
[gmx-users] Equilibration ‪farial tavakoli‬ ‪
[gmx-users] equilibration ‪farial tavakoli‬ ‪
[gmx-users] pdb2gmx ‪farial tavakoli‬ ‪
[gmx-users] ATB and PRODRG ‪farial tavakoli‬ ‪
[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy 刘玉杰
[gmx-users] gromacs rerun calculate the energy 王珍
[gmx-users] Generating GROMACS input file from the GAMESS output file 조영래
[gmx-users] Generating GROMACS input file from the GAMESS output file 조영래

Last message date: Mon Jul 31 23:19:23 CEST 2017
Archived on: Mon Jul 31 23:19:23 CEST 2017

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