gromacs.org_gmx-users

Messages by Date

2020/02/20 Re: [gmx-users] How to deal with unexpected reactions in umbrella sampling? Quyen V. Vu
2020/02/19 [gmx-users] gmx trjconv -force option doesn't seem to work. 고연주
2020/02/19 [gmx-users] cudaFuncGetAttributes failed: out of memory bonjour899
2020/02/19 [gmx-users] How to deal with unexpected reactions in umbrella sampling? Qing Lv
2020/02/19 Re: [gmx-users] How to cap a single residue in gromacs Quyen V. Vu
2020/02/19 Re: [gmx-users] GPU considerations for GROMACS Jason Hogrefe
2020/02/19 Re: [gmx-users] GPU considerations for GROMACS Kevin Boyd
2020/02/19 [gmx-users] Converting Charmm to gmx format using cgenff Maryam
2020/02/19 Re: [gmx-users] Selective RMSD calculation Bratin Kumar Das
2020/02/19 [gmx-users] Selective RMSD calculation Peter Mawanga
2020/02/19 Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) Sadaf Rani
2020/02/19 Re: [gmx-users] Increase Graphene sheet size Mohamed Abdelaal
2020/02/19 Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Alessandra Villa
2020/02/19 Re: [gmx-users] Increase Graphene sheet size Alessandra Villa
2020/02/19 Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Robert Cordina
2020/02/19 Re: [gmx-users] Increase Graphene sheet size Mohamed Abdelaal
2020/02/19 Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Alessandra Villa
2020/02/19 Re: [gmx-users] How to cap a single residue in gromacs Alessandra Villa
2020/02/19 Re: [gmx-users] Tabulated potentials Alessandra Villa
2020/02/18 [gmx-users] Regarding to pme on gpu Jimmy Chen
2020/02/18 [gmx-users] MolVA 2020 Deadline Extension (February 29th) - EuroVis 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data Björn Sommer
2020/02/18 [gmx-users] Problem in energy minimization and domain decomposition Sadaf Rani
2020/02/18 [gmx-users] Annealing Alex
2020/02/18 [gmx-users] Regarding to pme on gpu Jimmy Chen
2020/02/18 [gmx-users] How to cap a single residue in gromacs Sadaf Rani
2020/02/18 [gmx-users] GPU considerations for GROMACS hairul.ik...@gmail.com
2020/02/18 [gmx-users] CGENFF validation / optimization Adarsh V. K.
2020/02/18 [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Robert Cordina
2020/02/18 Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Luirink, R.A.
2020/02/18 Re: [gmx-users] Listing residues in gromacs Christian Blau
2020/02/18 [gmx-users] Listing residues in gromacs Subhomoi Borkotoky
2020/02/18 [gmx-users] Listing residues in gromacs Subhomoi Borkotoky
2020/02/18 Re: [gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU Szilárd Páll
2020/02/18 Re: [gmx-users] Tabulated potentials Ali Khodayari
2020/02/18 [gmx-users] Unexpected cudaStreamQuery failure: unspecified launch failure Mariem Ghoula
2020/02/18 Re: [gmx-users] Is Gromos force fields not recommended? Myunggi Yi
2020/02/18 Re: [gmx-users] Is Gromos force fields not recommended? Berk Hess
2020/02/18 Re: [gmx-users] Increase Graphene sheet size Alessandra Villa
2020/02/18 Re: [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation Alessandra Villa
2020/02/17 Re: [gmx-users] Is Gromos force fields not recommended? Bratin Kumar Das
2020/02/17 Re: [gmx-users] Is Gromos force fields not recommended? Mark Abraham
2020/02/17 Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU Navneet Kumar
2020/02/17 [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation bonjour899
2020/02/17 [gmx-users] Is Gromos force fields not recommended? Myunggi Yi
2020/02/17 Re: [gmx-users] Increase Graphene sheet size Dallas Warren
2020/02/17 [gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU Oliver Dutton
2020/02/17 [gmx-users] How to set restraints in free energy calculation? Sadaf Rani
2020/02/17 Re: [gmx-users] REMD stall out Daniel Burns
2020/02/17 Re: [gmx-users] REMD stall out Mark Abraham
2020/02/17 Re: [gmx-users] REMD stall out Szilárd Páll
2020/02/17 Re: [gmx-users] REMD stall out Daniel Burns
2020/02/17 Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU Christian Blau
2020/02/17 [gmx-users] CGENFF validation / optimization Adarsh V. K.
2020/02/17 Re: [gmx-users] (no subject) shakira shukoor
2020/02/17 Re: [gmx-users] (no subject) Christian Blau
2020/02/17 [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU Navneet Kumar
2020/02/17 Re: [gmx-users] REMD stall out Szilárd Páll
2020/02/17 Re: [gmx-users] Protein-Ligand Interaction calculation Justin Lemkul
2020/02/17 Re: [gmx-users] Protein-Ligand Interaction calculation Bratin Kumar Das
2020/02/17 Re: [gmx-users] Protein-Ligand Interaction calculation Александр Лашков
2020/02/17 [gmx-users] Protein-Ligand Interaction calculation Peter Mawanga
2020/02/17 [gmx-users] Increase Graphene sheet size Mohamed Abdelaal
2020/02/17 Re: [gmx-users] syntax error in GMXRC.csh in Gromacs2020 Paul Bauer
2020/02/17 Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Alessandra Villa
2020/02/17 [gmx-users] syntax error in GMXRC.csh in Gromacs2020 Harry Mark Greenblatt
2020/02/17 Re: [gmx-users] Cannot flush logfile - maybe you are out of disk space? Alessandra Villa
2020/02/17 Re: [gmx-users] Tabulated potentials Alessandra Villa
2020/02/16 [gmx-users] Cannot flush logfile - maybe you are out of disk space? Dilip.H.N
2020/02/16 Re: [gmx-users] LJ interactions in gromacs Kevin Boyd
2020/02/16 [gmx-users] LJ interactions in gromacs ??????
2020/02/16 Re: [gmx-users] Trajectory optimization - 2 chains are separated Dallas Warren
2020/02/16 Re: [gmx-users] Parametrization of Mn(ii) in charmm force field Justin Lemkul
2020/02/16 Re: [gmx-users] putting step wise constraints in energy minimization Justin Lemkul
2020/02/16 Re: [gmx-users] DEFORM option in gromacs Justin Lemkul
2020/02/16 [gmx-users] How to fix restraints in free energy calculation? Sadaf Rani
2020/02/16 [gmx-users] Parametrization of Mn(ii) in charmm force field Pranav BVN
2020/02/16 Re: [gmx-users] putting step wise constraints in energy minimization Sadaf Rani
2020/02/16 Re: [gmx-users] DEFORM option in gromacs shakira shukoor
2020/02/16 Re: [gmx-users] DEFORM option in gromacs Justin Lemkul
2020/02/16 [gmx-users] (no subject) shakira shukoor
2020/02/15 [gmx-users] DEFORM option in gromacs shakira shukoor
2020/02/15 Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 190, Issue 31 Shi Hailong
2020/02/15 Re: [gmx-users] Script for looping n simulations Justin Lemkul
2020/02/15 [gmx-users] Script for looping n simulations Neena Susan Eappen
2020/02/15 Re: [gmx-users] Trajectory optimization - 2 chains are separated Justin Lemkul
2020/02/15 Re: [gmx-users] problem while calculating order parameter Devargya Chakraborty
2020/02/15 Re: [gmx-users] Trajectory optimization - 2 chains are separated Marwa Abd El Kader
2020/02/15 Re: [gmx-users] problem while calculating order parameter Justin Lemkul
2020/02/15 Re: [gmx-users] putting step wise constraints in energy minimization Justin Lemkul
2020/02/15 Re: [gmx-users] problem while calculating order parameter shakira shukoor
2020/02/15 [gmx-users] problem while calculating order parameter Devargya Chakraborty
2020/02/14 [gmx-users] putting step wise constraints in energy minimization Sadaf Rani
2020/02/14 [gmx-users] how to apply constraints in energy minimization Sadaf Rani
2020/02/14 Re: [gmx-users] Ligand in PRODRG server is protonated. Why? Justin Lemkul
2020/02/14 Re: [gmx-users] Tabulated potentials Ali Khodayari
2020/02/14 [gmx-users] Ligand in PRODRG server is protonated. Why? Andrew Bostick
2020/02/14 Re: [gmx-users] Can't observe ion separation under the influence of electric field Man Hoang Viet
2020/02/14 Re: [gmx-users] grompp error : Atomtype HC not found Justin Lemkul
2020/02/14 Re: [gmx-users] Trajectory optimization - 2 chains are separated Justin Lemkul
2020/02/14 Re: [gmx-users] RNA md simulation Justin Lemkul
2020/02/14 Re: [gmx-users] (no subject) Justin Lemkul
2020/02/14 [gmx-users] grompp error : Atomtype HC not found Atila Petrosian
2020/02/14 [gmx-users] RNA md simulation Priyanka Singh
2020/02/14 Re: [gmx-users] Can't observe ion separation under the influence of electric field Live King
2020/02/13 Re: [gmx-users] Trajectory optimization - 2 chains are separated Marwa Abd El Kader
2020/02/13 Re: [gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics Paul bauer
2020/02/13 [gmx-users] (no subject) Neha Tiwari
2020/02/13 Re: [gmx-users] Trajectory optimization - 2 chains are separated Justin Lemkul
2020/02/13 Re: [gmx-users] grompp error : Atomtype HC not found Justin Lemkul
2020/02/13 Re: [gmx-users] genion without stdin Justin Lemkul
2020/02/13 [gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics Sadaf Rani
2020/02/13 [gmx-users] Trajectory optimization - 2 chains are separated Marwa Abd El Kader
2020/02/13 Re: [gmx-users] Can't observe ion separation under the influence of electric field Harutyun Sahakyan
2020/02/13 Re: [gmx-users] Tabulated potentials Alessandra Villa
2020/02/13 [gmx-users] grompp error : Atomtype HC not found Atila Petrosian
2020/02/13 Re: [gmx-users] genion without stdin Christian Blau
2020/02/13 [gmx-users] genion without stdin Urban, Matthias
2020/02/13 Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Luirink, R.A.
2020/02/12 Re: [gmx-users] Can't observe ion separation under the influence of electric field David van der Spoel
2020/02/12 Re: [gmx-users] Estimation of configurational entropy David van der Spoel
2020/02/12 [gmx-users] Estimation of configurational entropy Pathum Manjula Weerawarna
2020/02/12 [gmx-users] Can't observe ion separation under the influence of electric field Live King
2020/02/12 [gmx-users] Tabulated potentials Ali Khodayari
2020/02/12 [gmx-users] Test particle insertion in a specific region Sally Li
2020/02/12 Re: [gmx-users] generating Doxygen documentation Michele Pellegrino
2020/02/12 Re: [gmx-users] generating Doxygen documentation Paul Bauer
2020/02/12 Re: [gmx-users] generating Doxygen documentation Michele Pellegrino
2020/02/12 Re: [gmx-users] generating Doxygen documentation Michele Pellegrino
2020/02/12 Re: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020) Jihong Ma
2020/02/12 Re: [gmx-users] generating Doxygen documentation Sergio Perez
2020/02/12 Re: [gmx-users] generating Doxygen documentation Benson Muite
2020/02/12 [gmx-users] lmfit not working Sergio Perez
2020/02/12 Re: [gmx-users] runtime error: pdb2gmx issues in Python API Eric Irrgang
2020/02/12 Re: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020) Paul bauer
2020/02/12 [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020) Jihong Ma
2020/02/12 Re: [gmx-users] generating Doxygen documentation Mark Abraham
2020/02/12 [gmx-users] generating Doxygen documentation Michele Pellegrino
2020/02/12 Re: [gmx-users] Protein stabilization Justin Lemkul
2020/02/12 Re: [gmx-users] Experimental to Simulation Time Period Conversion Justin Lemkul
2020/02/12 Re: [gmx-users] Query Justin Lemkul
2020/02/12 Re: [gmx-users] Experimental to Simulation Time Period Conversion Peter Mawanga
2020/02/12 Re: [gmx-users] Experimental to Simulation Time Period Conversion John Whittaker
2020/02/12 [gmx-users] Protein stabilization Gonzalez Fernandez, Cristina
2020/02/12 [gmx-users] Experimental to Simulation Time Period Conversion Peter Mawanga
2020/02/12 Re: [gmx-users] Free energy perturbation of ligand Alessandra Villa
2020/02/11 Re: [gmx-users] simulation on graphite sheet Alessandra Villa
2020/02/11 [gmx-users] Free energy perturbation of ligand TIASHA ADHIKARY
2020/02/11 Re: [gmx-users] Query sai manohar
2020/02/11 [gmx-users] REMD stall out Daniel Burns
2020/02/11 [gmx-users] Python API Documentation question Marko Petrovic
2020/02/11 [gmx-users] simulation on graphite sheet Devargya Chakraborty
2020/02/11 [gmx-users] Query Neha Tiwari
2020/02/11 [gmx-users] density map calculation of lipid around 10 angstrom of protein SHAHEE ISLAM
2020/02/10 [gmx-users] Electric field settings in GROMACS Live King
2020/02/10 Re: [gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain Justin Lemkul
2020/02/10 Re: [gmx-users] problem with mpi run in REMD simulation Mark Abraham
2020/02/10 [gmx-users] Electron density profile calculation shakira shukoor
2020/02/10 [gmx-users] Viscosity calculations of gmx tcaf and gmx energy Mijiddorj B
2020/02/10 Re: [gmx-users] error found when doing tpi calculations Yakun
2020/02/09 Re: [gmx-users] problem with mpi run in REMD simulation Mohammad Madani
2020/02/09 Re: [gmx-users] Micellar shape Shan Jayasinghe
2020/02/09 Re: [gmx-users] problem with mpi run in REMD simulation Mark Abraham
2020/02/09 [gmx-users] problem with mpi run in REMD simulation Mohammad Madani
2020/02/08 Re: [gmx-users] Problem with mpirun Kevin Boyd
2020/02/08 [gmx-users] restraint-lambdas and bonded-lambdas for binding free energy calculations Qasim Pars
2020/02/08 [gmx-users] error found when doing tpi calculations Yakun
2020/02/07 [gmx-users] MARTINI forcefield shakira shukoor
2020/02/07 Re: [gmx-users] Graphene Sheet in GROMOS 54A7 Mohamed Abdelaal
2020/02/07 [gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain i . ilie
2020/02/07 Re: [gmx-users] How to use LBFGS minimization Alessandra Villa
2020/02/06 Re: [gmx-users] nrexcl for TIP4P-ICE water model Justin Lemkul
2020/02/06 Re: [gmx-users] Graphene Sheet in GROMOS 54A7 Bratin Kumar Das
2020/02/06 [gmx-users] nrexcl for TIP4P-ICE water model mbhendle
2020/02/06 Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Luirink, R.A.
2020/02/06 Re: [gmx-users] Gromacs question David van der Spoel
2020/02/06 [gmx-users] Problem with mpirun Seketoulie Keretsu
2020/02/06 Re: [gmx-users] adding an external body force Michele Pellegrino
2020/02/06 Re: [gmx-users] adding an external body force Justin Lemkul
2020/02/06 Re: [gmx-users] Energy plots for specific atoms/selections Justin Lemkul
2020/02/06 Re: [gmx-users] overriding -ignh flag Justin Lemkul
2020/02/06 Re: [gmx-users] modeling of zwitter-ions Justin Lemkul
2020/02/06 Re: [gmx-users] misunderstanding comm-grps Justin Lemkul
2020/02/06 Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Luirink, R.A.
2020/02/06 Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Luirink, R.A.
2020/02/06 Re: [gmx-users] How possible applying two different force field parameters for two-component in Gromacs simulation Dallas Warren
2020/02/06 [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Luirink, R.A.
2020/02/06 [gmx-users] adding an external body force Michele Pellegrino
2020/02/06 [gmx-users] How to use LBFGS minimization Bratin Kumar Das
2020/02/06 Re: [gmx-users] Energy plots for specific atoms/selections Bratin Kumar Das
2020/02/06 Re: [gmx-users] Question about gromacs mailing list Alessandra Villa
2020/02/05 [gmx-users] How possible applying two different force field parameters for two-component in Gromacs simulation mohammad torabi
2020/02/05 [gmx-users] : SOLVED GMX_MPI 2020 gmx_mpi segmentation fault Nicolas GOUDARD
2020/02/05 Re: [gmx-users] RDF calculation from surface of protein ISHRAT JAHAN
2020/02/05 Re: [gmx-users] overriding -ignh flag Yogesh Sharma
2020/02/05 [gmx-users] Question about gromacs mailing list and configurational entropy Amit Kumar
2020/02/05 [gmx-users] modeling of zwitter-ions Olga Selyutina
2020/02/05 Re: [gmx-users] misunderstanding comm-grps Miro Astore
2020/02/05 [gmx-users] RDF calculation from surface of protein Pandya, Akash
2020/02/05 Re: [gmx-users] How to add two different "defaults" parameters in topology file Justin Lemkul
2020/02/05 Re: [gmx-users] overriding -ignh flag Justin Lemkul