[gmx-users] problem in NPT equilibration step

Dear Gromacs user, I am trying to simulate a protein (nmr structure).I have successfully done energy minimisation step.Also I have equilibrated the system a 298 k (which is achieved from 100 ps run) .Now,I am trying to equilibrate the system at 1 bar pressure.After a run of 100 ps ,I am getting av

[gmx-users] Fwd: do_dssp

-- Forwarded message -- From: Preeti Choudhary Date: Tue, May 14, 2013 at 8:30 PM Subject: do_dssp To: Discussion list for GROMACS users I am facing problem while using do_dssp.I need to store secondary structure data every 100 ps.For this I am using -dt option.But I didn'

[gmx-users] do_dssp

I am facing problem while using do_dssp.I -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the lis

Re: [gmx-users] g_cluster warning

t; completely different, for the gro file I get 42 while for the tpr file I > > get 2 clusters. > > > > Does anybody know why this is the case? > > > > Cheers > > Sabine > > > > > > > > On 05/10/2013 04:33 PM, Preeti Choudhary wrote: > &g

[gmx-users] g_cluster warning

hello everyone I am trying to cluster my data using g_cluster.I simulated the whole protein. I did the g_cluster analysis with only certain region of the protein which I specified using an index file.The program runs fine and gives 1 cluster.My concern is the warning it gives which states that :-

Re: [gmx-users] random seed in molecular dynamics

check the code to see what it does if you use grompp -t). > tprconv does not follow it. > > The random seed is in a different variable, but only does anything if > gen_vel=yes. > > I am not sure what the basis of your confusion about repeated calls to > grompp is. > >

[gmx-users] random seed in molecular dynamics

hey this is regarding random seed used in md.this is when it selects the intial velocity and selects from maxwell-istribution.but is it selects only once or selects this random seed every time when grompp makes .tpr file.really confused about this random seed concept.can u clear my confusion?? -th

Re: [gmx-users] Fwd: rmsd

Thankyou On Wed, Apr 10, 2013 at 11:30 PM, Justin Lemkul wrote: > On Wed, Apr 10, 2013 at 10:43 AM, Preeti Choudhary < > preetichoudhary18111...@gmail.com> wrote: > > > -- Forwarded message ------ > > From: Preeti Choudhary > > Date: Wed, Apr 10,

[gmx-users] Fwd: rmsd

-- Forwarded message -- From: Preeti Choudhary Date: Wed, Apr 10, 2013 at 7:46 PM Subject: rmsd To: gmx-users-ow...@gromacs.org Hi, I calculated the rmsd of my md simulation trajectory by giving the tpr file I used as an input in for my final mdrun.I am getting rmsd of about 5