Re: [gmx-users] bug in demux.pl

I should have looked at the format when it writes the time but thanks for your help. -Swarnendu On Tue, Aug 2, 2011 at 7:07 PM, Mark Abraham wrote: > On 3/08/2011 8:19 AM, Swarnendu Tripathi wrote: > > Hi, > > I am not sure if this problem has been solved or discussed before. &

[gmx-users] bug in demux.pl

Hi, I am not sure if this problem has been solved or discussed before. I found that when I use the demux.pl script it does not read the actual time from the .log file. This is for gromacs-4.0.7. These are few lines from one of the .log file for my replica exchnage simulation. For example in the

Re: [gmx-users] unit of ekrot and ektrans

Thanks. I got it. I was using gnuplot before. -Swarnendu On Tue, May 31, 2011 at 3:45 PM, Dommert Florian < domm...@icp.uni-stuttgart.de> wrote: > On Tue, 2011-05-31 at 15:31 -0400, Swarnendu Tripathi wrote: > > Hello everybody, > > > > I have a question ragarding th

[gmx-users] unit of ekrot and ektrans

Hello everybody, I have a question ragarding the unit of translational and rotational energy. I am using the gromacs-4.0.7 version and it gives these units in the ektran.xvg and ekrot.xvg as "kJ mol\S-1\N" after I used the command" g_traj -f traj.trr -s topol.trr -ekt ektrans.xvg -ekr ekrot.xvg. I

Re: [gmx-users] No cut-off

Thank you very much. Really very helpful comments. -Swarnendu On Thu, Mar 24, 2011 at 1:52 AM, Mark Abraham wrote: > On 24/03/2011 4:38 PM, Swarnendu Tripathi wrote: > > Hi all, > > Thank you for the reply. The answer I got for the second question about > table-extension

Re: [gmx-users] No cut-off

gt; >> grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should stick >> to it. >> >> Cheers, >> Itamar >> >> On 24/03/11 1:13 PM, Swarnendu Tripathi wrote: >> >>> Hello everybody, >>> >>> I want to use the no cut-of

[gmx-users] No cut-off

Hello everybody, I want to use the no cut-off option in gromacs for the electrostatic interactions. In manual it says for this I need to define: pbc=no; nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file. My questions are: 1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a

Re: [gmx-users] Coulomb interactions

Thank you very much. I thought gromacs should do that but also a very useful suggestion for checking that. -Swarnendu On Mon, Mar 14, 2011 at 9:54 PM, Mark Abraham wrote: > > > On 15/03/11, *Swarnendu Tripathi * wrote: > > Hello everyone, > > In gromacs when the Cou

[gmx-users] Coulomb interactions

Hello everyone, In gromacs when the Coulomb interactions are calculated are they calculated for the all atom pairs or only for the charged atoms pairs? If the Coulomb interactions are not calculated only for the charged atoms then how can I modify the gromacs to do that. In my system I have only

Re: [gmx-users] rlist and rcoulomb

Hello, Thanks for the reply. So, can I think that when I set rcoulomb > rlist then the Coulomb (LR) energy term is providing some kind of correction over the Coulomb (SR) energy term. -Swarnendu On Thu, Oct 21, 2010 at 4:39 PM, Justin A. Lemkul wrote: > > > Swarnendu Tr

[gmx-users] rlist and rcoulomb

Dear gromacs users, In section 4.6.3 of gromacs 4 manual it says ``... the interactions between pairs that do not fall within rlist but do fall within max(rcoulomb,rvdw) are computed during neighbor search (NS), and the forces and energy are stored separately, and added to short-range forces at ev