Re: [gmx-users] Scaled 1-5 interactions

Florian Dommert wrote: * Mark Abraham [2009-06-05 10:31:22 +1000]: Borys Szefczyk wrote: Dear GROMACS Users, I would like to use the OPLS force field, but with additional scaling factor for the Coulomb 1-5 interactions for certain atoms. More precisely, I want to use the standard 0.5 scalin

Re: SV: SV: [gmx-users] diffusion coefficient with g_msd

Sarah Witzke wrote: Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have post

SV: SV: [gmx-users] diffusion coefficient with g_msd

Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: > Dear XAvier, > > > > Thank you very much for your answer. I have posted my .mdp file i

Re: [gmx-users] Scaled 1-5 interactions

* Mark Abraham [2009-06-05 10:31:22 +1000]: Borys Szefczyk wrote: Dear GROMACS Users, I would like to use the OPLS force field, but with additional scaling factor for the Coulomb 1-5 interactions for certain atoms. More precisely, I want to use the standard 0.5 scaling for Coulomb and LJ 1-4

Re: [gmx-users] Pressure and NVT Simulations

On Sat, 2009-06-06 at 00:30 +0530, Manik Mayur wrote: > On Fri, Jun 5, 2009 at 11:58 PM, Jussi Lehtola > wrote: > Generally speaking, if your density is too small, the system > wants to > increase it and thus you have negative pressure. If it is too > large, >

Re: [gmx-users] Pressure and NVT Simulations

On Fri, Jun 5, 2009 at 11:58 PM, Jussi Lehtola wrote: > On Fri, 2009-06-05 at 23:28 +0530, Manik Mayur wrote: > > Hi, > > I am trying to equilibrate a box of SPC/E water using NVT simulations. > > After 2 ns of equilibration my pressure is still <0 bars. Is it an > > expected behavior for NVT simu

Re: [gmx-users] Pressure and NVT Simulations

On Fri, 2009-06-05 at 23:28 +0530, Manik Mayur wrote: > Hi, > I am trying to equilibrate a box of SPC/E water using NVT simulations. > After 2 ns of equilibration my pressure is still <0 bars. Is it an > expected behavior for NVT simulations or the pressure should converge > to the thermodynamic eq

[gmx-users] Pressure and NVT Simulations

Hi, I am trying to equilibrate a box of SPC/E water using NVT simulations. After 2 ns of equilibration my pressure is still <0 bars. Is it an expected behavior for NVT simulations or the pressure should converge to the thermodynamic equilibration value corresponding to T and density after a finite

Re: [gmx-users] conversion to tip5p

Dmitri Dubov wrote: Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top , but when I apply similar c

Re: [gmx-users] conversion to tip5p

2009/6/5 Dmitri Dubov > Hi, all > > > Using gromacs 3.3 I try to work with tip5 water, but I fail to convert > water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is > easy with pdb2gmx > > > pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top > Does it really con

Re: SV: [gmx-users] diffusion coefficient with g_msd

Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mod

[gmx-users] conversion to tip5p

Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top , but when I apply similar command for tip5p, the output

SV: [gmx-users] diffusion coefficient with g_msd

Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mode= Linear

Re: [gmx-users] g_hbond error

Justin A. Lemkul skrev: krishnakumar wrote: Hi, Has any one encountered this error while using g_hbond? * Select a group: 12 Selected 12: 'SOL' Select a group: 12 Selected 12: 'SOL' Calculating hydrogen bonds in SOL (20949

Re: [gmx-users] Scaled 1-5 interactions

On Fri, Jun 05, 2009 at 10:31:22AM +1000, Mark Abraham wrote: > Setting the number of exclusions for a moleculetype to 4, in a forcefield > with "generate_pairs = yes" and "fudgeLJ = 0.5" will probably see pdb2gmx > get everything except the 1-5 interactions right. Then you post-process the > .t

Re: [gmx-users] diffusion coefficient with g_msd

On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd.