gromacs.org_gmx-users
Thread
Date
Earlier messages
Later messages
Messages by Thread
Re: [gmx-users] Is Gromos force fields not recommended?
Mark Abraham
Re: [gmx-users] Is Gromos force fields not recommended?
Bratin Kumar Das
Re: [gmx-users] Is Gromos force fields not recommended?
Berk Hess
Re: [gmx-users] Is Gromos force fields not recommended?
Myunggi Yi
[gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU
Oliver Dutton
Re: [gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU
Szilárd Páll
Re: [gmx-users] Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU
Oliver Dutton
[gmx-users] How to set restraints in free energy calculation?
Sadaf Rani
[gmx-users] CGENFF validation / optimization
Adarsh V. K.
[gmx-users] CGENFF validation / optimization
Adarsh V. K.
Re: [gmx-users] CGENFF validation / optimization
Justin Lemkul
[gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU
Navneet Kumar
Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU
Christian Blau
Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU
Navneet Kumar
[gmx-users] Protein-Ligand Interaction calculation
Peter Mawanga
Re: [gmx-users] Protein-Ligand Interaction calculation
Александр Лашков
Re: [gmx-users] Protein-Ligand Interaction calculation
Bratin Kumar Das
Re: [gmx-users] Protein-Ligand Interaction calculation
Justin Lemkul
[gmx-users] Increase Graphene sheet size
Mohamed Abdelaal
Re: [gmx-users] Increase Graphene sheet size
Dallas Warren
Re: [gmx-users] Increase Graphene sheet size
Alessandra Villa
Re: [gmx-users] Increase Graphene sheet size
Mohamed Abdelaal
Re: [gmx-users] Increase Graphene sheet size
Alessandra Villa
Re: [gmx-users] Increase Graphene sheet size
Mohamed Abdelaal
[gmx-users] syntax error in GMXRC.csh in Gromacs2020
Harry Mark Greenblatt
Re: [gmx-users] syntax error in GMXRC.csh in Gromacs2020
Paul Bauer
[gmx-users] Cannot flush logfile - maybe you are out of disk space?
Dilip.H.N
Re: [gmx-users] Cannot flush logfile - maybe you are out of disk space?
Alessandra Villa
[gmx-users] LJ interactions in gromacs
??????
Re: [gmx-users] LJ interactions in gromacs
Kevin Boyd
[gmx-users] How to fix restraints in free energy calculation?
Sadaf Rani
[gmx-users] Parametrization of Mn(ii) in charmm force field
Pranav BVN
Re: [gmx-users] Parametrization of Mn(ii) in charmm force field
Justin Lemkul
[gmx-users] Parametrization of Mn(ii) in charmm force field
Pranav BVN
Re: [gmx-users] Parametrization of Mn(ii) in charmm force field
Alessandra Villa
Re: [gmx-users] Parametrization of Mn(ii) in charmm force field
Justin Lemkul
[gmx-users] DEFORM option in gromacs
shakira shukoor
Re: [gmx-users] DEFORM option in gromacs
Justin Lemkul
Re: [gmx-users] DEFORM option in gromacs
shakira shukoor
Re: [gmx-users] DEFORM option in gromacs
Justin Lemkul
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 190, Issue 31
Shi Hailong
[gmx-users] Script for looping n simulations
Neena Susan Eappen
Re: [gmx-users] Script for looping n simulations
Justin Lemkul
Re: [gmx-users] Script for looping n simulations
Neena Susan Eappen
Re: [gmx-users] Script for looping n simulations
Neena Susan Eappen
Re: [gmx-users] Script for looping n simulations
Neena Susan Eappen
Re: [gmx-users] Script for looping n simulations
Justin Lemkul
Re: [gmx-users] Script for looping n simulations
Justin Lemkul
Re: [gmx-users] Script for looping n simulations
Miro Astore
[gmx-users] problem while calculating order parameter
Devargya Chakraborty
Re: [gmx-users] problem while calculating order parameter
shakira shukoor
Re: [gmx-users] problem while calculating order parameter
Justin Lemkul
Re: [gmx-users] problem while calculating order parameter
Devargya Chakraborty
[gmx-users] putting step wise constraints in energy minimization
Sadaf Rani
Re: [gmx-users] putting step wise constraints in energy minimization
Justin Lemkul
Re: [gmx-users] putting step wise constraints in energy minimization
Sadaf Rani
Re: [gmx-users] putting step wise constraints in energy minimization
Justin Lemkul
[gmx-users] how to apply constraints in energy minimization
Sadaf Rani
[gmx-users] Ligand in PRODRG server is protonated. Why?
Andrew Bostick
Re: [gmx-users] Ligand in PRODRG server is protonated. Why?
Justin Lemkul
Re: [gmx-users] Can't observe ion separation under the influence of electric field
Man Hoang Viet
[gmx-users] RNA md simulation
Priyanka Singh
Re: [gmx-users] RNA md simulation
Justin Lemkul
Re: [gmx-users] RNA md simulation
Priyanka Singh
[gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics
Sadaf Rani
Re: [gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics
Paul bauer
[gmx-users] Trajectory optimization - 2 chains are separated
Marwa Abd El Kader
Re: [gmx-users] Trajectory optimization - 2 chains are separated
Justin Lemkul
Re: [gmx-users] Trajectory optimization - 2 chains are separated
Marwa Abd El Kader
Re: [gmx-users] Trajectory optimization - 2 chains are separated
Justin Lemkul
Re: [gmx-users] Trajectory optimization - 2 chains are separated
Marwa Abd El Kader
Re: [gmx-users] Trajectory optimization - 2 chains are separated
Justin Lemkul
Re: [gmx-users] Trajectory optimization - 2 chains are separated
Dallas Warren
[gmx-users] grompp error : Atomtype HC not found
Atila Petrosian
Re: [gmx-users] grompp error : Atomtype HC not found
Justin Lemkul
[gmx-users] grompp error : Atomtype HC not found
Atila Petrosian
Re: [gmx-users] grompp error : Atomtype HC not found
Justin Lemkul
[gmx-users] genion without stdin
Urban, Matthias
Re: [gmx-users] genion without stdin
Christian Blau
Re: [gmx-users] genion without stdin
Justin Lemkul
[gmx-users] Estimation of configurational entropy
Pathum Manjula Weerawarna
Re: [gmx-users] Estimation of configurational entropy
David van der Spoel
[gmx-users] Can't observe ion separation under the influence of electric field
Live King
Re: [gmx-users] Can't observe ion separation under the influence of electric field
David van der Spoel
Re: [gmx-users] Can't observe ion separation under the influence of electric field
Harutyun Sahakyan
Re: [gmx-users] Can't observe ion separation under the influence of electric field
Live King
[gmx-users] Tabulated potentials
Ali Khodayari
Re: [gmx-users] Tabulated potentials
Alessandra Villa
Re: [gmx-users] Tabulated potentials
Ali Khodayari
Re: [gmx-users] Tabulated potentials
Alessandra Villa
Re: [gmx-users] Tabulated potentials
Ali Khodayari
Re: [gmx-users] Tabulated potentials
Alessandra Villa
[gmx-users] Test particle insertion in a specific region
Sally Li
[gmx-users] lmfit not working
Sergio Perez
[gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020)
Jihong Ma
Re: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020)
Paul bauer
Re: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020)
Jihong Ma
[gmx-users] generating Doxygen documentation
Michele Pellegrino
Re: [gmx-users] generating Doxygen documentation
Mark Abraham
Re: [gmx-users] generating Doxygen documentation
Benson Muite
Re: [gmx-users] generating Doxygen documentation
Sergio Perez
Re: [gmx-users] generating Doxygen documentation
Michele Pellegrino
Re: [gmx-users] generating Doxygen documentation
Michele Pellegrino
Re: [gmx-users] generating Doxygen documentation
Paul Bauer
Re: [gmx-users] generating Doxygen documentation
Michele Pellegrino
[gmx-users] Protein stabilization
Gonzalez Fernandez, Cristina
Re: [gmx-users] Protein stabilization
Justin Lemkul
[gmx-users] Experimental to Simulation Time Period Conversion
Peter Mawanga
Re: [gmx-users] Experimental to Simulation Time Period Conversion
John Whittaker
Re: [gmx-users] Experimental to Simulation Time Period Conversion
Peter Mawanga
Re: [gmx-users] Experimental to Simulation Time Period Conversion
Justin Lemkul
[gmx-users] Free energy perturbation of ligand
TIASHA ADHIKARY
Re: [gmx-users] Free energy perturbation of ligand
Alessandra Villa
[gmx-users] REMD stall out
Daniel Burns
Re: [gmx-users] REMD stall out
Szilárd Páll
Re: [gmx-users] REMD stall out
Daniel Burns
Re: [gmx-users] REMD stall out
Szilárd Páll
Re: [gmx-users] REMD stall out
Mark Abraham
Re: [gmx-users] REMD stall out
Daniel Burns
Re: [gmx-users] REMD stall out
Daniel Burns
Re: [gmx-users] REMD stall out
Daniel Burns
[gmx-users] Python API Documentation question
Marko Petrovic
[gmx-users] simulation on graphite sheet
Devargya Chakraborty
Re: [gmx-users] simulation on graphite sheet
Alessandra Villa
[gmx-users] Query
Neha Tiwari
Re: [gmx-users] Query
sai manohar
Re: [gmx-users] Query
Justin Lemkul
[gmx-users] density map calculation of lipid around 10 angstrom of protein
SHAHEE ISLAM
[gmx-users] Electric field settings in GROMACS
Live King
[gmx-users] Electron density profile calculation
shakira shukoor
[gmx-users] Viscosity calculations of gmx tcaf and gmx energy
Mijiddorj B
[gmx-users] problem with mpi run in REMD simulation
Mohammad Madani
Re: [gmx-users] problem with mpi run in REMD simulation
Mark Abraham
Re: [gmx-users] problem with mpi run in REMD simulation
Mohammad Madani
Re: [gmx-users] problem with mpi run in REMD simulation
Mark Abraham
[gmx-users] restraint-lambdas and bonded-lambdas for binding free energy calculations
Qasim Pars
[gmx-users] error found when doing tpi calculations
Yakun
Re: [gmx-users] error found when doing tpi calculations
Yakun
[gmx-users] MARTINI forcefield
shakira shukoor
[gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain
i . ilie
Re: [gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain
Justin Lemkul
[gmx-users] nrexcl for TIP4P-ICE water model
mbhendle
Re: [gmx-users] nrexcl for TIP4P-ICE water model
Justin Lemkul
Re: [gmx-users] Gromacs question
David van der Spoel
[gmx-users] Problem with mpirun
Seketoulie Keretsu
Re: [gmx-users] Problem with mpirun
Kevin Boyd
[gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Luirink, R.A.
Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Luirink, R.A.
Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Luirink, R.A.
Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Luirink, R.A.
Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Luirink, R.A.
Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Alessandra Villa
Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Luirink, R.A.
[gmx-users] adding an external body force
Michele Pellegrino
Re: [gmx-users] adding an external body force
Justin Lemkul
Re: [gmx-users] adding an external body force
Michele Pellegrino
[gmx-users] How to use LBFGS minimization
Bratin Kumar Das
Re: [gmx-users] How to use LBFGS minimization
Alessandra Villa
Re: [gmx-users] Question about gromacs mailing list
Alessandra Villa
[gmx-users] How possible applying two different force field parameters for two-component in Gromacs simulation
mohammad torabi
Re: [gmx-users] How possible applying two different force field parameters for two-component in Gromacs simulation
Dallas Warren
[gmx-users] Question about gromacs mailing list and configurational entropy
Amit Kumar
[gmx-users] modeling of zwitter-ions
Olga Selyutina
Re: [gmx-users] modeling of zwitter-ions
Justin Lemkul
[gmx-users] RDF calculation from surface of protein
Pandya, Akash
Re: [gmx-users] RDF calculation from surface of protein
ISHRAT JAHAN
[gmx-users] What is the difference between density of states (gmx dos) and vibrational power spectrum (gmx velacc -os)?
Kneller, Daniel
Re: [gmx-users] What is the difference between density of states (gmx dos) and vibrational power spectrum (gmx velacc -os)?
David van der Spoel
[gmx-users] overriding -ignh flag
Yogesh Sharma
Re: [gmx-users] overriding -ignh flag
Justin Lemkul
Re: [gmx-users] overriding -ignh flag
Yogesh Sharma
Re: [gmx-users] overriding -ignh flag
Justin Lemkul
[gmx-users] How to add two different "defaults" parameters in topology file
mbhendle
Re: [gmx-users] How to add two different "defaults" parameters in topology file
Justin Lemkul
[gmx-users] Gromacs bug related to rms and atommass.dat interplay (Can not find mass in database for atom MG in residue)
Vedat Durmaz
Re: [gmx-users] Gromacs bug related to rms and atommass.dat interplay (Can not find mass in database for atom MG in residue)
Justin Lemkul
[gmx-users] Micellar shape
Shan Jayasinghe
Re: [gmx-users] Micellar shape
Justin Lemkul
Re: [gmx-users] Micellar shape
Shan Jayasinghe
[gmx-users] runtime error: pdb2gmx issues in Python API
Marko Petrovic
Re: [gmx-users] runtime error: pdb2gmx issues in Python API
Marko Petrovic
Re: [gmx-users] runtime error: pdb2gmx issues in Python API
Eric Irrgang
[gmx-users] Graphene Sheet in GROMOS 54A7
Mohamed Abdelaal
Re: [gmx-users] Graphene Sheet in GROMOS 54A7
Dallas Warren
Re: [gmx-users] Graphene Sheet in GROMOS 54A7
Bratin Kumar Das
Re: [gmx-users] Graphene Sheet in GROMOS 54A7
Mohamed Abdelaal
[gmx-users] Analysis using sh file
ric.concu
Re: [gmx-users] Analysis using sh file
Alessandra Villa
[gmx-users] Selecting water molecules within a nanotube
RAHUL SURESH
Re: [gmx-users] Selecting water molecules within a nanotube
Alessandra Villa
[gmx-users] Generate the Topology with CGenFF :: Error message
Adarsh V. K.
[gmx-users] Generate the Topology with CGenFF :: Error message - CGenFF versions are not equivalent! :: *.str 4.0 and charmm36-mar2019.ff/forcefield.doc : 4.1 are not equivalent!
Adarsh V. K.
[gmx-users] Generate the Topology with CGenFF :: Error message - CGenFF versions are not equivalent! :: *.str 4.0 and charmm36-mar2019.ff/forcefield.doc : 4.1 are not equivalent!
Adarsh V. K.
Re: [gmx-users] Generate the Topology with CGenFF :: Error message
Justin Lemkul
[gmx-users] Regarding calculation of configurational entropy
Amit Kumar
Re: [gmx-users] Regarding calculation of configurational entropy
David van der Spoel
[gmx-users] misunderstanding comm-grps
Miro Astore
Re: [gmx-users] misunderstanding comm-grps
Dallas Warren
Re: [gmx-users] misunderstanding comm-grps
Justin Lemkul
Re: [gmx-users] misunderstanding comm-grps
Miro Astore
Earlier messages
Later messages