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Starting: Sun May 1 13:48:55 CEST 2016
Ending: Tue May 31 23:16:18 CEST 2016
Messages: 610

[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 1 Marzieh Saeedi Masineh
[gmx-users] Moving this mailing list to Discourse format Szilárd Páll
[gmx-users] gmx distance h.alizadeh at znu.ac.ir
[gmx-users] bond_atomtype Ming Tang
[gmx-users] Choosing water molecules and box type and dimensions zeineb SI CHAIB
[gmx-users] Generating topology for Tetrahydrofolate within CHARMM ff zeineb SI CHAIB
[gmx-users] Comparison of diffusion constant from Einstein and Green Kubo abhishek khetan
[gmx-users] bond_atomtype Justin Lemkul
[gmx-users] Generating topology for Tetrahydrofolate within CHARMM ff zeineb SI CHAIB
[gmx-users] Generating topology for Tetrahydrofolate within CHARMM ff Justin Lemkul
[gmx-users] bond_atomtype Ming Tang
[gmx-users] Using ORCA with Gromacs bharat gupta
[gmx-users] problems in MPI run for REMD in GROMACS Pabitra Mohan
[gmx-users] Building and Equilibrating a United-Atom DOPC-DPPC-Cholesterol Bilayer John Smith
[gmx-users] problems in MPI run for REMD in GROMACS Terry
[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 4 Pabitra Mohan
[gmx-users] cisplatin charmm36 parameter Nikhil Maroli
[gmx-users] Residue not found in residue topology database Md. Imrul Reza Shishir
[gmx-users] Residue not found in residue topology database Mark Abraham
[gmx-users] simulation in urea Divya Dube
[gmx-users] Starting residue "XXX"in chain not identified as Protein/RNA/DNA. Md. Imrul Reza Shishir
[gmx-users] Starting residue "XXX"in chain not identified as Protein/RNA/DNA. Nikhil Maroli
[gmx-users] cisplatin charmm36 parameter Justin Lemkul
[gmx-users] Relative binding free energy from a neutral to a charged molecule Stefania Evoli
[gmx-users] gmx hbond - specify precise atom names involved Nash, Anthony
[gmx-users] unsuscribe Wood Irene
[gmx-users] gmx hbond - specify precise atom names involved Nash, Anthony
[gmx-users] Fw: MDsimulation of Protein-DNA complex soumi
[gmx-users] Fw: MDsimulation of Protein-DNA complex soumi
[gmx-users] MDsimulation of Protein-DNA complex soumi
[gmx-users] gmx hbond - specify precise atom names involved Justin Lemkul
[gmx-users] unsuscribe Justin Lemkul
[gmx-users] MDsimulation of Protein-DNA complex terrencesun at gmail.com
[gmx-users] pdb2gmx assign CSER to non-terminal serine Zheng Ruan
[gmx-users] pdb2gmx assign CSER to non-terminal serine Justin Lemkul
[gmx-users] pdb2gmx assign CSER to non-terminal serine Zheng Ruan
[gmx-users] gmx hbond - specify precise atom names involved Nash, Anthony
[gmx-users] gmx hbond - specify precise atom names involved Justin Lemkul
[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs Pedro Lacerda
[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs Pedro Lacerda
[gmx-users] Umbrella sampling version 5.0 Steve Seibold
[gmx-users] Umbrella sampling version 5.0 Justin Lemkul
[gmx-users] Relative FEP topology question - What to do with state B dummy atoms in the .itp file under [ bonds ], [ angles ] and [ dihedrals ] Billy Noonan
[gmx-users] Relative FEP topology question - What to do with state B dummy atoms in the .itp file under [ bonds ], [ angles ] and [ dihedrals ] hannes.loeffler at stfc.ac.uk
[gmx-users] restraints definition in mdp Sana Saeed
[gmx-users] pdb2gmx -ignh Alexander Alexander
[gmx-users] pdb2gmx -ignh Justin Lemkul
[gmx-users] restraints definition in mdp Justin Lemkul
[gmx-users] persistent jumps in trajectories morpheus
[gmx-users] restraints definition in mdp Justin Lemkul
[gmx-users] persistent jumps in trajectories Justin Lemkul
[gmx-users] restarts ingram
[gmx-users] restarts Justin Lemkul
[gmx-users] do_dssp strange reaction Chalaoux, Francois-Regis
[gmx-users] do_dssp strange reaction Justin Lemkul
[gmx-users] How to Compile tools without mpi ? Chalaoux, Francois-Regis
[gmx-users] How to Compile tools without mpi ? Mark Abraham
[gmx-users] How to Compile tools without mpi ? Mark Abraham
[gmx-users] How to Compile tools without mpi ? Chalaoux, Francois-Regis
[gmx-users] urea simulation and hdb definition Divya Dube
[gmx-users] two molecules in a single topology file Chang Woon Jang
[gmx-users] RE GROMAC Free Energy Question on Topologies hannes.loeffler at stfc.ac.uk
[gmx-users] angle type error Williams Miranda
[gmx-users] angle type error Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 12 Sana Saeed
[gmx-users] angle type error Williams Miranda
[gmx-users] simulation Self assembly monolayers with OPLS-TIP3P (CPU and GUP) Pratiti Bhadra
[gmx-users] CHARMM-GUI Membrane building problems John Smith
[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 12 jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] gromacs warning topology file naming residues Upasana Ray
[gmx-users] gromacs warning topology file naming residues Justin Lemkul
[gmx-users] simulation Self assembly monolayers with OPLS-TIP3P (CPU and GUP) Justin Lemkul
[gmx-users] Need for REMD equil.mdp and sim.mdp files Pabitra Mohan
[gmx-users] gromacs warning topology file naming residues Upasana Ray
[gmx-users] gromacs warning topology file naming residues Justin Lemkul
[gmx-users] Need for REMD equil.mdp and sim.mdp files Justin Lemkul
[gmx-users] simulation Self assembly monolayers with OPLS-TIP3P (CPU and GUP) Mark Abraham
[gmx-users] How to Compile tools without mpi ? Mark Abraham
[gmx-users] Suggested settings for using Amber force field in Gromacs Casalini Tommaso
[gmx-users] Suggested settings for using Amber force field in Gromacs Dries Van Rompaey
[gmx-users] How to Compile tools without mpi ? Chalaoux, Francois-Regis
[gmx-users] Suggested settings for using Amber force field in Gromacs Casalini Tommaso
[gmx-users] Suggested settings for using Amber force field in Gromacs Justin Lemkul
[gmx-users] Suggested settings for using Amber force field in Gromacs Hannes Loeffler
[gmx-users] Suggested settings for using Amber force field in Gromacs Casalini Tommaso
[gmx-users] merging two topol file Alexander Alexander
[gmx-users] gmx distance Teemu Murtola
[gmx-users] Two molecules in a single topology file Chang Woon Jang
[gmx-users] CHARMM-GUI Membrane building problems John Smith
[gmx-users] (no subject) Rishikesh Parulekar
[gmx-users] gromacs fftw installation Neha Gandhi
[gmx-users] gromacs fftw installation Erik Marklund
[gmx-users] g_wham: How to get the umbrella positions from pullf.xvg when pull-start = no? Liping Sunshine
[gmx-users] on atom types related to ligand Brett
[gmx-users] Pabitra Mohan needs help in installing Gromacs5.1.2 Pabitra Mohan
[gmx-users] Pabitra Mohan needs help in installing Gromacs5.1.2 Mark Abraham
[gmx-users] Pabitra Mohan needs help in installing Gromacs5.1.2 Mark Abraham
[gmx-users] extend phosphorylated simulation 43A1p Mehreen Jan
[gmx-users] CHARMM-GUI Membrane building problems Justin Lemkul
[gmx-users] on atom types related to ligand Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] CHARMM-GUI Membrane building problems Björn Sommer
[gmx-users] (no subject) Rishikesh Parulekar
[gmx-users] Protein Ligand simulation Alex Mathew
[gmx-users] Using Poisson mean field approximation for electrostatic interactions Sikandar Mashayak
[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs João M. Damas
[gmx-users] Two [ defaults ] sections Alexander Alexander
[gmx-users] Two [ defaults ] sections Justin Lemkul
[gmx-users] Protein Ligand simulation Alex Mathew
[gmx-users] Protein Ligand simulation Justin Lemkul
[gmx-users] gromacs fftw installation Christoph Junghans
[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs Peter Stern
[gmx-users] Relative binding free energy from a neutral to a charged molecule Christopher Neale
[gmx-users] Full precision distance calculation Parvez Mh
[gmx-users] Relative binding free energy from a neutral to a charged molecule hannes.loeffler at stfc.ac.uk
[gmx-users] Full precision distance calculation Justin Lemkul
[gmx-users] peptide into surface Alexander Alexander
[gmx-users] TPO and SEP is is added in residue.date Mehreen Jan
[gmx-users] order parameter of carbon bonds 凌未风
[gmx-users] water model mahdiyeh poorsargol
[gmx-users] water model Erik Marklund
[gmx-users] LINCS WARRING PROBLEM Upasana Ray
[gmx-users] Fixing the center of mass Alexander Alexander
[gmx-users] water model mahdiyeh poorsargol
[gmx-users] Analysis of protein protein interaction James Starlight
[gmx-users] LINCS WARRING PROBLEM Mark Abraham
[gmx-users] force calculation mahdiyeh poorsargol
[gmx-users] calculate electrostatic force masoud keramati
[gmx-users] TPO and SEP is is added in residue.date Justin Lemkul
[gmx-users] Fixing the center of mass Justin Lemkul
[gmx-users] force calculation Justin Lemkul
[gmx-users] on editconf Brett
[gmx-users] on editconf Justin Lemkul
[gmx-users] qm/mm Jacopo Sgrignani
[gmx-users] invalid order of directive atomtypes Brett
[gmx-users] invalid order of directive atomtypes Justin Lemkul
[gmx-users] force calculation mahdiyeh poorsargol
[gmx-users] GPU/CPU perfomance loss Van Zyl, J, Mnr <justinvz at sun.ac.za>
[gmx-users] Minimization of Cyclohexane Trappe United Atom doerrstein at posteo.de
[gmx-users] memory error Clinton King
[gmx-users] residue UNK not found- how to generate force field parameters? Jacob Nowatzke
[gmx-users] residue UNK not found- how to generate force field parameters? Justin Lemkul
[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs Pedro Lacerda
[gmx-users] Convert gro into psf Roshan Shrestha
[gmx-users] Convert gro into psf Roshan Shrestha
[gmx-users] gromacs on multiple gpus Neha Gandhi
[gmx-users] H definition in urea topology file buildup Divya Dube
[gmx-users] gromacs on multiple gpus Kutzner, Carsten
[gmx-users] gromacs on multiple gpus Mark Abraham
[gmx-users] qmmm question andrian
[gmx-users] Convert gro into psf Justin Lemkul
[gmx-users] Convert gro into psf Roshan Shrestha
[gmx-users] Fwd: CUDA compilation problem for Gromacs 5.1.2 (with fix) Sjoerd de Vries
[gmx-users] Fwd: CUDA compilation problem for Gromacs 5.1.2 (with fix) Mark Abraham
[gmx-users] Fwd: CUDA compilation problem for Gromacs 5.1.2 (with fix) Sjoerd de Vries
[gmx-users] Fwd: CUDA compilation problem for Gromacs 5.1.2 (with fix) Sjoerd de Vries
[gmx-users] Fwd: CUDA compilation problem for Gromacs 5.1.2 (with fix) Mark Abraham
[gmx-users] Fwd: CUDA compilation problem for Gromacs 5.1.2 (with fix) Sjoerd de Vries
[gmx-users] Convert gro into psf Justin Lemkul
[gmx-users] Fwd: CUDA compilation problem for Gromacs 5.1.2 (with fix) Mark Abraham
[gmx-users] Fwd: CUDA compilation problem for Gromacs 5.1.2 (with fix) Szilárd Páll
[gmx-users] gmx solvate Alexander Alexander
[gmx-users] Surface tension Ganesh Shahane
[gmx-users] GPU/CPU perfomance loss Szilárd Páll
[gmx-users] GPU/CPU perfomance loss Szilárd Páll
[gmx-users] gmx solvate Mark Abraham
[gmx-users] gmx-users qmmm question (andrian) Groenhof, Gerrit
[gmx-users] GPU/CPU perfomance loss Mark Abraham
[gmx-users] gmx solvate Alexander Alexander
[gmx-users] gmx solvate Mark Abraham
[gmx-users] Does Non-Protein include SOL? Irem Altan
[gmx-users] Does Non-Protein include SOL? Justin Lemkul
[gmx-users] Surface tension André Farias de Moura
[gmx-users] on the itp file Brett
[gmx-users] on the itp file Justin Lemkul
[gmx-users] Minimization error Abid Channa
[gmx-users] on "Invalid order for directive defaults" Brett
[gmx-users] on "Invalid order for directive defaults" Justin Lemkul
[gmx-users] Surface tension Ganesh Shahane
[gmx-users] problem to continue MD run Williams Miranda
[gmx-users] GPUs performance on Gromacs calculation Ming Tang
[gmx-users] on HS14 atomtype Brett
[gmx-users] how to order gpus on different nodes Ming Tang
[gmx-users] on HS14 atomtype Sarath Chandra
[gmx-users] GPUs performance on Gromacs calculation Mark Abraham
[gmx-users] how to order gpus on different nodes Mark Abraham
[gmx-users] problem to continue MD run Mark Abraham
[gmx-users] on HS14 atomtype Brett
[gmx-users] on HS14 atomtype Sarath Chandra
[gmx-users] choosing box type Upasana Ray
[gmx-users] choosing box type Justin Lemkul
[gmx-users] OpenMP ingram
[gmx-users] Generating topology for a heme protein zeineb SI CHAIB
[gmx-users] Generating topology for a HEM protein with CHARMM27 zeineb SI CHAIB
[gmx-users] Generating topology for a HEM protein with CHARMM27 Justin Lemkul
[gmx-users] on atomtypes Brett
[gmx-users] on atomtypes Justin Lemkul
[gmx-users] on atomtypes Brett
[gmx-users] on atomtypes Justin Lemkul
[gmx-users] GROMACS 2016-beta1 released Mark Abraham
[gmx-users] GROMACS 2016-beta1 released Nikhil Maroli
[gmx-users] Hydrophobic interaction analysis Nikhil Maroli
[gmx-users] problem to continue MD run Williams Miranda
[gmx-users] problem to continue MD run Mark Abraham
[gmx-users] problem to continue MD run Williams Miranda
[gmx-users] problem to continue MD run Williams Miranda
[gmx-users] Making separate topology file for QM atoms bharat gupta
[gmx-users] REMD on more than one node YanhuaOuyang
[gmx-users] Regarding Dynamic cross correlation map analysis soumi
[gmx-users] PME and particle insertion Jakob Wohlert
[gmx-users] REMD on more than one node Mark Abraham
[gmx-users] REMD error YanhuaOuyang
[gmx-users] REMD error Mark Abraham
[gmx-users] REMD error YanhuaOuyang
[gmx-users] REMD error Mark Abraham
[gmx-users] Making separate topology file for QM atoms (bharat gupta) Groenhof, Gerrit
[gmx-users] Generating topology for a HEM protein with CHARMM27 zeineb SI CHAIB
[gmx-users] Re. Generating topology for Tetrahydrofolate within CHARMM ff zeineb SI CHAIB
[gmx-users] Gromacs installation. Elsaid Younes
[gmx-users] Hydrophobic interaction analysis Sun Iba
[gmx-users] Re. Generating topology for Tetrahydrofolate within CHARMM ff Justin Lemkul
[gmx-users] Hydrophobic interaction analysis Nikhil Maroli
[gmx-users] Gromacs installation. Szilárd Páll
[gmx-users] pdb2gmx error after switching force fields Irem Altan
[gmx-users] pdb2gmx error after switching force fields Justin Lemkul
[gmx-users] Hydrophobic interaction analysis Justin Lemkul
[gmx-users] pdb2gmx error after switching force fields Irem Altan
[gmx-users] pdb2gmx error after switching force fields Justin Lemkul
[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein Antara mazumdar
[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein Mark Abraham
[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein Antara mazumdar
[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein Tsjerk Wassenaar
[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein Antara mazumdar
[gmx-users] md-vv integrator on gromacs 4.5.5 LiYao
[gmx-users] md-vv integrator on gromacs 4.5.5 Justin Lemkul
[gmx-users] Restart simulation from checkpoint file with fewer nodes Husen R
[gmx-users] Restart simulation from checkpoint file with fewer nodes Husen R
[gmx-users] Restart simulation from checkpoint file with fewer nodes Justin Lemkul
[gmx-users] Restart simulation from checkpoint file with fewer nodes Husen R
[gmx-users] Restart simulation from checkpoint file with fewer nodes jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] md-vv integrator on gromacs 4.5.5 Yao Li
[gmx-users] warning 1-4 interaction in QMMM simulation andrian
[gmx-users] (no subject) Upasana Ray
[gmx-users] simulation_time Ms. Nikita Bora
[gmx-users] (no subject) Tsjerk Wassenaar
[gmx-users] Restart simulation from checkpoint file with fewer nodes Husen R
[gmx-users] (no subject) Chalaoux, Francois-Regis
[gmx-users] simulation_time Justin Lemkul
[gmx-users] Restart simulation from checkpoint file with fewer nodes Justin Lemkul
[gmx-users] (no subject) Upasana Ray
[gmx-users] (no subject) Chalaoux, Francois-Regis
[gmx-users] (no subject) Pratiti Bhadra
[gmx-users] Restart simulation from checkpoint file with fewer nodes jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL Antara mazumdar
[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL Mark Abraham
[gmx-users] Restart simulation from checkpoint file with fewer nodes Mark Abraham
[gmx-users] (no subject) Upasana Ray
[gmx-users] (no subject) Mark Abraham
[gmx-users] (no subject) Francesco Carbone
[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL Mark Abraham
[gmx-users] COM-Pull along a direction Pengzhi Zhang
[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL Justin Lemkul
[gmx-users] Umbrella Sampling - choice of pull-coord?-dim Lukas Zimmermann
[gmx-users] PCA and FEL sun
[gmx-users] PCA and FEL Tsjerk Wassenaar
[gmx-users] PCA and FEL sun
[gmx-users] PCA and FEL Tsjerk Wassenaar
[gmx-users] PCA and FEL sun
[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 55 Antara mazumdar
[gmx-users] Restart simulation from checkpoint file with fewer nodes jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] How to visualize the Free Energy Landscape file generated by g_sham sun
[gmx-users] Restart simulation from checkpoint file with fewer nodes Mark Abraham
[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL Justin Lemkul
[gmx-users] Restart simulation from checkpoint file with fewer nodes jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] simulation_time Ms. Nikita Bora
[gmx-users] How to create a spherocylindrical wall jagannath mondal
[gmx-users] How to create a spherocylindrical wall Jagannath Mondal
[gmx-users] Removing periodic boundary condition Sanket Ghawali
[gmx-users] Calculating Distance Sanket Ghawali
[gmx-users] Calculating Distance masoud keramati
[gmx-users] Removing periodic boundary condition Tsjerk Wassenaar
[gmx-users] Restart simulation from checkpoint file with fewer nodes Husen R
[gmx-users] heat of vaporization Saitama Lawliet
[gmx-users] simulation_time Justin Lemkul
[gmx-users] Calculating Distance Justin Lemkul
[gmx-users] tutor/speptide Alexander Alexander
[gmx-users] tutor/speptide Justin Lemkul
[gmx-users] improper .gro file format generated by trjconv Esra Kaçar
[gmx-users] problem with MPI,thread and number of CPU khourshaeishargh at mech.sharif.ir
[gmx-users] problem with MPI,thread and number of CPU Mark Abraham
[gmx-users] Checking PMF convergenece using WHAM Khuong Truong Gia
[gmx-users] Minimization error Abid Channa
[gmx-users] Generating topology for Tetrahydrofolate within CHARMM ff zeineb SI CHAIB
[gmx-users] improper .gro file format generated by trjconv Mark Abraham
[gmx-users] Checking PMF convergenece using WHAM Catarina A. Carvalheda dos Santos
[gmx-users] Pull code slows down mdrun -- is this expected? Christopher Neale
[gmx-users] Pull code slows down mdrun -- is this expected? Christopher Neale
[gmx-users] Calculating Distance Christopher Neale
[gmx-users] Pull code slows down mdrun -- is this expected? Mark Abraham
[gmx-users] Pull code slows down mdrun -- is this expected? Christopher Neale
[gmx-users] Pull code slows down mdrun -- is this expected? Christopher Neale
[gmx-users] Pull code slows down mdrun -- is this expected? Mark Abraham
[gmx-users] Pull code slows down mdrun -- is this expected? Christopher Neale
[gmx-users] Checking PMF convergenece using WHAM Khuong Truong Gia
[gmx-users] Pull code slows down mdrun -- is this expected? Szilárd Páll
[gmx-users] Pull code slows down mdrun -- is this expected? Szilárd Páll
[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 61 Sanket Ghawali
[gmx-users] Calculating Distance Sanket Ghawali
[gmx-users] Calculating Distance Tsjerk Wassenaar
[gmx-users] Production run error Sanket Ghawali
[gmx-users] Production run error Tsjerk Wassenaar
[gmx-users] simulation_time Ms. Nikita Bora
[gmx-users] query amir zeb
[gmx-users] query Nikhil Maroli
[gmx-users] Free energy - Methane in water Alexander Alexander
[gmx-users] query Erik Marklund
[gmx-users] simulation_time Tsjerk Wassenaar
[gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS. Barrett Worley
[gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS. André Farias de Moura
[gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS. Barrett Worley
[gmx-users] Free energy - Methane in water Justin Lemkul
[gmx-users] Gromacs installation. Elsaid Younes
[gmx-users] Help required for calculation of protein coverage % wrt time Antara mazumdar
[gmx-users] Help required for calculation of protein coverage % wrt time Sarath Chandra
[gmx-users] Generating topology for a hem protein zeineb SI CHAIB
[gmx-users] Generating topology for a hem protein Justin Lemkul
[gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS. André Farias de Moura
[gmx-users] Help required for calculation of protein coverage % wrt time Tsjerk Wassenaar
[gmx-users] Pull code slows down mdrun -- is this expected? Christopher Neale
[gmx-users] Help required for calculation of protein coverage % wrt time Antara mazumdar
[gmx-users] help required in calculating npme value for domain decomposition Antara mazumdar
[gmx-users] simulation_time[Nikita Bora] Ms. Nikita Bora
[gmx-users] help required in calculating npme value for domain decomposition Sarath Chandra
[gmx-users] simulation_time[Nikita Bora] Tsjerk Wassenaar
[gmx-users] Regarding installation of gromacs SOUVIK MONDAL
[gmx-users] Analysis SOUVIK MONDAL
[gmx-users] Analysis jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] Analysis SOUVIK MONDAL
[gmx-users] Analysis Justin Lemkul
[gmx-users] grompp_d and mdrun_d in gromacs 5.1.2 Emma Ahlstrand
[gmx-users] OPLS problem Steve Seibold
[gmx-users] grompp_d and mdrun_d in gromacs 5.1.2 jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] OPLS problem Christopher Neale
[gmx-users] OPLS problem Christopher Neale
[gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS. Barrett Worley
[gmx-users] g_dos to calculate the heat capacity from a simulation of TIP4P water Sal Lim
[gmx-users] make_ndx treats "&" and "AND" differently -- expected? Christopher Neale
[gmx-users] grompp_d and mdrun_d in gromacs 5.1.2 Mark Abraham
[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid? Christopher Neale
[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid? Justin Lemkul
[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid? Mark Abraham
[gmx-users] Protein-membrane simulation error. BIJENDRA KHADKA
[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid? Christopher Neale
[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid? Teemu Murtola
[gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr Antara mazumdar
[gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr Tsjerk Wassenaar
[gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr Tsjerk Wassenaar
[gmx-users] help required in plotting percentage of protein in contact with membrane vs time Antara mazumdar
[gmx-users] help required in plotting percentage of protein in contact with membrane vs time Justin Lemkul
[gmx-users] Protein-membrane simulation error. Justin Lemkul
[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr Antara mazumdar
[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr Justin Lemkul
[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr Mark Abraham
[gmx-users] Analyse REMD YanhuaOuyang
[gmx-users] please help Saheen Shehnaz
[gmx-users] Adding ions mohammad r
[gmx-users] query on implementation details of flat-bottomed potential Jagannath Mondal
[gmx-users] g_cluster analysis SAPNA BORAH
[gmx-users] g_cluster analysis Tsjerk Wassenaar
[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr Antara mazumdar
[gmx-users] find out tpx version of tpr Sabine Reisser
[gmx-users] Generating topology for a HEM protein with CHARMM27 zeineb SI CHAIB
[gmx-users] find out tpx version of tpr Mark Abraham
[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr Mark Abraham
[gmx-users] find out tpx version of tpr Tsjerk Wassenaar
[gmx-users] find out tpx version of tpr Sabine Reisser
[gmx-users] uninstall gromacs 5.0 Anurag Dobhal
[gmx-users] Doubt regarding extracting energy component while pull code is applied. Tushar Ranjan Moharana
[gmx-users] uninstall gromacs 5.0 Mark Abraham
[gmx-users] ERROR in Membrane-protein simulation BIJENDRA KHADKA
[gmx-users] uninstall gromacs 5.0 sun
[gmx-users] uninstall gromacs 5.0 Mark Abraham
[gmx-users] ERROR in Membrane-protein simulation Mark Abraham
[gmx-users] uninstall gromacs 5.0 sun
[gmx-users] uninstall gromacs 5.0 sun
[gmx-users] uninstall gromacs 5.0 sun
[gmx-users] uninstall gromacs 5.0 Anurag Dobhal
[gmx-users] Combining various Flat-bottomed Potentials Srajan Jain
[gmx-users] ffbonded.itp a.omidi at shirazu.ac.ir
[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system Antara mazumdar
[gmx-users] Deprotonated Asp and Glu sun
[gmx-users] Deprotonated Asp and Glu sun
[gmx-users] Deprotonated Asp and Glu Justin Lemkul
[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system Justin Lemkul
[gmx-users] ffbonded.itp Justin Lemkul
[gmx-users] Deprotonated Asp and Glu Smith, Micholas D.
[gmx-users] Generating topology for a HEM protein with CHARMM27 Justin Lemkul
[gmx-users] Deprotonated Asp and Glu sun
[gmx-users] SAS for membrane protein Maximilien LOPES RODRIGUES
[gmx-users] SAS for membrane protein Justin Lemkul
[gmx-users] ?==?utf-8?q? SAS for membrane protein Maximilien LOPES RODRIGUES
[gmx-users] SAS for membrane protein Justin Lemkul
[gmx-users] angle_restraint_z Karina
[gmx-users] angle_restraint_z Justin Lemkul
[gmx-users] QMMM grompp error atom numbers fields. Melchor S.
[gmx-users] small molecule aggregation analysis Surahit Chewle
[gmx-users] Combining various Flat-bottomed Potentials Christopher Neale
[gmx-users] Combining various Flat-bottomed Potentials Justin Lemkul
[gmx-users] small molecule aggregation analysis Justin Lemkul
[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid? Christopher Neale
[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid? Teemu Murtola
[gmx-users] Release of FESetup 1.2 Hannes Loeffler
[gmx-users] Combining various Flat-bottomed Potentials Christopher Neale
[gmx-users] Combining various Flat-bottomed Potentials Christopher Neale
[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges Sourav Ray
[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges Mark Abraham
[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges Sourav Ray
[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges Sourav Ray
[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges Justin Lemkul
[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges Tsjerk Wassenaar
[gmx-users] Simulating conjugated protein Sanket Ghawali
[gmx-users] Combining various Flat-bottomed Potentials jagannath mondal
[gmx-users] Combining various Flat-bottomed Potentials Jagannath Mondal
[gmx-users] QMMM grompp error atom numbers fields. Groenhof, Gerrit
[gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel Antara mazumdar
[gmx-users] Installing GROMACS 5.1.2 om GPU יוכבד
[gmx-users] a suitable forcefield for ions mah maz
[gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel Mark Abraham
[gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD Wang Tao
[gmx-users] Installing GROMACS 5.1.2 om GPU Mark Abraham
[gmx-users] Unusual bond Alexander Alexander
[gmx-users] a suitable forcefield for ions Erik Marklund
[gmx-users] Unusual bond Justin Lemkul
[gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD Justin Lemkul
[gmx-users] Combining various Flat-bottomed Potentials Justin Lemkul
[gmx-users] Simulating conjugated protein Justin Lemkul
[gmx-users] a suitable forcefield for ions mah maz
[gmx-users] a suitable forcefield for ions Justin Lemkul
[gmx-users] a suitable forcefield for ions mah maz
[gmx-users] a suitable forcefield for ions Justin Lemkul
[gmx-users] a suitable forcefield for ions Nilkanta Chowdhury
[gmx-users] a suitable forcefield for ions Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 93 Wang Tao
[gmx-users] Surface tension coupling with Parrinello-Rahman algorithm Giuseppe Léonardo Licari
[gmx-users] Generating topology for a HEM protein with CHARMM27 zeineb SI CHAIB
[gmx-users] restraints between two different molecules Rebeca García Fandiño
[gmx-users] restraints between two different molecules Mark Abraham
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Szilárd Páll
[gmx-users] Surface tension coupling with Parrinello-Rahman algorithm André Farias de Moura
[gmx-users] Surface tension coupling with Parrinello-Rahman algorithm Giuseppe Léonardo Licari
[gmx-users] Force Field for amino acid and peptide Alexander Alexander
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD Justin Lemkul
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Szilárd Páll
[gmx-users] Generating topology for a HEM protein with CHARMM27 Justin Lemkul
[gmx-users] Force Field for amino acid and peptide Justin Lemkul
[gmx-users] Apply position restraints to part of RNA molecule 闫舒婷
[gmx-users] simulation_time[Nikita Bora] SAPNA BORAH
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel Antara mazumdar
[gmx-users] Ion flux through membrane protein Maximilien LOPES RODRIGUES
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel Mark Abraham
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel Mark Abraham
[gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD Mark Abraham
[gmx-users] simulation_time[Nikita Bora] Mark Abraham
[gmx-users] Ion flux through membrane protein Kutzner, Carsten
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel Antara mazumdar
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel Mark Abraham
[gmx-users] gmx gangle failure after assigning zero-charges Thomas Niklas
[gmx-users] Installing GROMACS 5.1.2 om GPU יוכבד
[gmx-users] Installing GROMACS 5.1.2 om GPU Mark Abraham
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel Antara mazumdar
[gmx-users] Calculate total non-bonded contacts in gromacs SAPNA BORAH
[gmx-users] Extending the MD sun
[gmx-users] Extending the MD SAPNA BORAH
[gmx-users] Extending the MD sun
[gmx-users] Extending the MD SAPNA BORAH
[gmx-users] Extending the MD sun
[gmx-users] simulation_time[Nikita Bora] SAPNA BORAH
[gmx-users] Extending the MD SAPNA BORAH
[gmx-users] Extending the MD SAPNA BORAH
[gmx-users] simulation_time[Nikita Bora] Justin Lemkul
[gmx-users] Calculate total non-bonded contacts in gromacs Justin Lemkul
[gmx-users] Extending the MD sun
[gmx-users] Extending the MD SAPNA BORAH
[gmx-users] Ion flux through membrane protein Maximilien LOPES RODRIGUES
[gmx-users] liquid-solid/liquid-air interface simulations liu junjun
[gmx-users] free energy calculation on amino acid mutation Yi An
[gmx-users] free energy calculation on amino acid mutation Yi An
[gmx-users] free energy calculation on amino acid mutation hannes.loeffler at stfc.ac.uk
[gmx-users] free energy calculation on amino acid mutation Mark Abraham
[gmx-users] Relaxation Test khourshaeishargh at mech.sharif.ir
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Mark Abraham
[gmx-users] Lipid Head group Orientation Nidhin Thomas
[gmx-users] Distance restraint and pull code HongTham
[gmx-users] liquid-solid/liquid-air interface simulations André Farias de Moura
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) Naga Sundar
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Mark Abraham
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) Nikhil Maroli
[gmx-users] restraints between two different molecules Rebeca García Fandiño
[gmx-users] Force Field for amino acid and peptide Alexander Alexander
[gmx-users] Ion flux through membrane protein Nikhil Maroli
[gmx-users] Force Field for amino acid and peptide Mark Abraham
[gmx-users] amidated C-terminal residue of peptide kamakshi sikka
[gmx-users] gratitude DOCENTE ANTISTIO ANIBAL ALVIS AMADOR
[gmx-users] NMA problems with mass-weighting -m option Ravasio Riccardo
[gmx-users] NEMD khourshaeishargh at mech.sharif.ir
[gmx-users] Lipid Head group Orientation Chandan Choudhury
[gmx-users] NEMD Mark Abraham
[gmx-users] Output of g energy khourshaeishargh at mech.sharif.ir
[gmx-users] amidated C-terminal residue of peptide Justin Lemkul
[gmx-users] Distance restraint and pull code Justin Lemkul
[gmx-users] restraints between two different molecules Justin Lemkul
[gmx-users] Output of g energy Justin Lemkul
[gmx-users] NEMD khourshaeishargh at mech.sharif.ir
[gmx-users] Output of g energy khourshaeishargh at mech.sharif.ir
[gmx-users] Conversion from GROMACS .top .itp to CHARMM .psf .par combo Sourav Ray
[gmx-users] Lipid Head group Orientation Nidhin Thomas
[gmx-users] query on performance of GTX 1080 in gromacs Jagannath Mondal
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] query on performance of GTX 1080 in gromacs Mark Abraham
[gmx-users] 'gmx rdf' and 'gmx select' questions Eric Smoll
[gmx-users] gmx density question Eric Smoll
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Szilárd Páll
[gmx-users] Lipid Head group Orientation Thomas Piggot
[gmx-users] gmx traj Eric Smoll
[gmx-users] gmx traj Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 109 kamakshi sikka
[gmx-users] fe4s4 Nilkanta Chowdhury
[gmx-users] query on performance of GTX 1080 in gromacs Jagannath Mondal
[gmx-users] Adaptive Biasing Force method khourshaeishargh at mech.sharif.ir
[gmx-users] amidated C-terminal residue of peptide Justin Lemkul
[gmx-users] fe4s4 Justin Lemkul
[gmx-users] Adaptive Biasing Force method Justin Lemkul
[gmx-users] fe4s4 Nilkanta Chowdhury
[gmx-users] fe4s4 Mark Abraham
[gmx-users] Fwd: Conversion from GROMACS .top .itp to CHARMM .psf .par combo Sourav Ray
[gmx-users] Suggestion required for calculation of membrane contact sites and Lipid binding strength Antara mazumdar
[gmx-users] Fwd: Conversion from GROMACS .top .itp to CHARMM .psf .par combo Michael Shirts
[gmx-users] NMA problems with mass-weighting -m option Tsjerk Wassenaar
[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 111 Nidhin Thomas
[gmx-users] fe4s4 Ullmann, Thomas
[gmx-users] Software inconsistency error: pme_loadbal_do called at an interval != nstlist Yorquant Wang
[gmx-users] poor average exchange ratio for each replica YanhuaOuyang
[gmx-users] amidated C-terminal residue of peptide kamakshi sikka
[gmx-users] 'gmx rdf' and 'gmx select' questions Teemu Murtola
[gmx-users] Free Energy Topology between A and B. Nash, Anthony
[gmx-users] Free Energy Topology between A and B. Justin Lemkul
[gmx-users] Free Energy Topology between A and B. Nash, Anthony
[gmx-users] NMA problems with mass-weighting -m option Ravasio Riccardo
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] calculating Dielectric constant Life Sciences Inc
[gmx-users] Calculating Dielectric constant Life Sciences Inc
[gmx-users] Calculating Dielectric constant Justin Lemkul
[gmx-users] trjconv -dump buffer overflow Marlon Sidore
[gmx-users] Grompp error Anurag Dobhal
[gmx-users] Topology of a neutral single peptide soumadwip ghosh
[gmx-users] Topology of a neutral single peptide Justin Lemkul
[gmx-users] Grompp error Justin Lemkul
[gmx-users] Grompp error Anurag Dobhal
[gmx-users] Grompp error Justin Lemkul
[gmx-users] Grompp error Anurag Dobhal
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Szilárd Páll
[gmx-users] protonating GLUs Irem Altan
[gmx-users] protonating GLUs Justin Lemkul
[gmx-users] protonating GLUs Irem Altan
[gmx-users] protonating GLUs Justin Lemkul
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] How to generate opls aa parameters for new element myself? Wang Tao
[gmx-users] Analyse REMD Christopher Neale
[gmx-users] Gromacs 5.1 I/O strategy Andreas Mecklenfeld
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Mark Abraham
[gmx-users] Angle between a vector and the normal to a sphere ABEL Stephane 175950
[gmx-users] Confusion regarding creation of .itp file Apramita Chand
[gmx-users] Confusion regarding creation of .itp file Apramita Chand
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Mark Abraham
[gmx-users] Angle between a vector and the normal to a sphere Yu Ogawa
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Uliano Guerrini
[gmx-users] Calculating Dielectric constant Life Sciences Inc
[gmx-users] Density of States syntax question Chapman, Christopher W.
[gmx-users] Density of States syntax question Marcelo Depólo
[gmx-users] GROMACS 2016-beta2 released Mark Abraham
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Diogo Martins de Sá
[gmx-users] Angle between a vector and the normal to a sphere ABEL Stephane 175950
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Nikhil Maroli
[gmx-users] [gmx-developers] GTX 680 non detected on OS X Szilárd Páll
[gmx-users] Confusion regarding creation of .itp file Nikhil Maroli
[gmx-users] Confusion regarding creation of .itp file Mark Abraham
[gmx-users] Confusion regarding creation of .itp file Mark Abraham
[gmx-users] Gromacs 5.1 I/O strategy Mark Abraham
[gmx-users] How to generate opls aa parameters for new element myself? Mark Abraham
[gmx-users] How to generate opls aa parameters for new element myself? Mark Abraham
[gmx-users] trjconv -dump buffer overflow Mark Abraham
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Diogo Martins de Sá
[gmx-users] How to generate opls aa parameters for new element myself? Clinton King
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Florent Hédin
[gmx-users] Calculating Dielectric constant David van der Spoel
[gmx-users] Calculating Dielectric constant David van der Spoel
[gmx-users] Density of States syntax question Chapman, Christopher W.
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Diogo Martins de Sá
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Szilárd Páll
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Szilárd Páll
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Szilárd Páll
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Szilárd Páll
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Fabricio Cannini
[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1 Mark Abraham

Last message date: Tue May 31 23:16:18 CEST 2016
Archived on: Tue May 31 23:16:20 CEST 2016

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