[gmx-users] water box size from output files

Hi I was wondering if there is a way to determine the water box size from the output files after the simulation run is over Thanks Rabab Toubar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] water box size from output files

Thanks Justin for your reply. But what is the extension of the output coordinate file. And for the .edr file it failed to open in windows; how can I possibly view it Thanks Rabab Toubar --- On Mon, 7/25/11, Justin A. Lemkul wrote: > From: Justin A. Lemkul > Subject: Re: [gmx-users]

[gmx-users] Twin-range cut-off

Does anyone has a clear definition or a reference for the Twin-range cut-off? I searched the internet and looked at the manual yet I couldn't get the idea   Thanks Rabab Toubar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

[gmx-users] Position restraint for 2ns

if we define -DPOSRES My question is the run ended very quickly that doesn't seem 2ns for me. I apologize if it is a silly question but I have just strated using GMX Thanks Rabab Toubar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] 1-4 interaction not within cut-off

Hi, I set my .mdp file to minimize the system for 1000 steps, but it stopped at ~200 saying: "Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10" but the molecule is now outside the box I did position restraint for 2ns using

Re: [gmx-users] 1-4 interaction not within cut-off

e-5    ; bar-1 ref_p   =  1.0 ; Generate velocites is on at 300 K. gen_vel =  yes gen_temp    =  300.0 gen_seed    = 621432 Any suggestions are appreciated Thanks Rabab Toubar --- On Thu, 6/3/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject:

Re: [gmx-users] 1-4 interaction not within cut-off

ations went well till the end of the 25 ns run! But seems that mine is crashing. Any suggestions? Thanks Rabab Toubar --- On Fri, 6/4/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] 1-4 interaction not within cut-off To: "Gromacs Users' List" Dat

Re: [gmx-users] 1-4 interaction not within cut-off

ll restraints were then removed, and the simulations were carried out. " Thanks Rabab Toubar --- On Fri, 6/4/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] 1-4 interaction not within cut-off To: "Gromacs Users' List" Date: Friday, June 4, 2010,

[gmx-users] tracking the time for an md run

Hi, Can anyone let me know how to know how long the md run would take, or how long is left. I tried tailing it, but couldn't find a time factor there Thanks Rabab -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the ar

[gmx-users] top2psf.pl

Hi Trying to use top2psf.pl, as suggested Usage: top2psf.pl -i (topology filename) -o (output filename) but I get an error message saying invalid command name "top2psf.pl" Suggestions? Thanks Rabab -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

[gmx-users] trjconv index file

Trying to extract the protein from the md run without waters, all the mailing lists suggests using an index file before running trjconv, but I get file input/output error Can someone give me more details on how to egt the index file thanks Rabab -- gmx-users mailing listgmx-

Re: [gmx-users] trjconv index file

Hi, I want to extract the protein only without the waters. And from the mailing list discussing trjconv, what I did was: make_ndx -f conf-protein trajconv -f pr.trr -n index.ndx -o pr_trj.trr , but I get file input/output error Am I missing something? Thanks Rabab Toubar --- On Tue, 6/15

Re: [gmx-users] trjconv index file

Rabab Toubar --- On Wed, 6/16/10, Justin A. Lemkul wrote: > From: Justin A. Lemkul > Subject: Re: [gmx-users] trjconv index file > To: "Discussion list for GROMACS users" > Date: Wednesday, June 16, 2010, 7:26 AM > > > Rabab Toubar wrote: > > Hi, &

[gmx-users] Forcefields for proteins

I came across this paper for the ff G45a3 and it says that is good for aliphatics, so I was wondering if there is a forcefield that is recommended to be used in case of proteins simulations in water. Rabab Toubar -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Re: His protonation

So is there a way we can make His neutral before running the simulations as in case of NAMD? Rabab Toubar --- On Wed, 6/16/10, Justin A. Lemkul wrote: > From: Justin A. Lemkul > Subject: [gmx-users] Re: His protonation > To: "sagar barage" , "Gromacs Users' List

[gmx-users] System net charge

I have noticed that you get the overall charge WHILE you are setting up the system - when using grompp I think. Now if after the mdrun and I want to check the overall charge, how can I possibly do that? I tried the mailing list but didn't find an answer to my question Thanks Rabab T

[gmx-users] Plotting Energies versus time

Hi, I want to extract the values for potential E, kinetic E, total E, and temperature from the log file so as to plot them versus time. In NAMD it is easy to do that using cat |grep, is there a similar way to do it in GMX Thanks Rabab Toubar -- gmx-users mailing listgmx-users

[gmx-users] How to tell if the molecule is correctly reduced?

Hi I did simulations for a protein with disulfide bonds using opls. Then I reduced the ssbonds in vmd and did simulations for the reduced. When loading gro(or pdb) and trr files on vmd I do not see reduced bonds. I also compared the two pdb files and they looked the same in terms of number of h

Re: [gmx-users] How to tell if the molecule is correctly reduced?

confirm that the molecule is properly reduced Rabab Toubar --- On Wed, 8/25/10, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] How to tell if the molecule is correctly reduced? To: "Discussion list for GROMACS users" Date: Wednesday, August 25, 2010, 8:57 PM