[gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04
chatterjee_paulami at yahoo.co.in
Fri Jul 10 12:53:13 CEST 2015
Thank you Justin for the suggestion. I was able to obtain a full trajectory using trjcat.
However I would also like to mention that the exact commands I have shown in my previous mails produced the files with 'the names'.
Can you please tell me if I want to have the full trajectory from the extension what changes should be made in the command line?Should I use
gmx convert-tpr -s md_0_1.tpr -extend 70000 -o final_monomer.tpr
gmx mdrun -s final_monomer.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append
Thanks and Regards,Paulami
On Friday, 10 July 2015 2:13 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
On 7/9/15 3:09 PM, PAULAMI CHATTERJEE wrote:
> I have used the following commands for the initial mdrun
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
> gmx mdrun -deffnm md_0_1
> Can you please suggest now what went wrong?
So you have a trajectory named md_0_1.xtc - that should contain the first part
of the run. Then somehow you say you've got traj_comp.xtc (though none of the
commands you've shown would produce a file with that name), so if that's the case:
gmx trjcat -f md_0_1.xtc traj_comp.xtc -o full.xtc
That will have the whole thing.
> On Thursday, 9 July 2015 5:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 7/9/15 4:15 AM, PAULAMI CHATTERJEE wrote:
> > Dear All,
> > I have a 30 ns trajectory which I would like to extend up to 100 ns. For that
> I gave the following commands
> > gmx convert-tpr -s md_0_1.tpr -extend 70000 -o final_monomer.tpr
> > gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append
> > After completion of the extension two new trajectory files were generated-
> 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the
> trajectory with
> > gmxcheck -f traj_comp.xtc
> > the output is
> > Checking file traj_comp.xtc
> > Reading frame 0 time 30000.000
> > # Atoms 16867
> > Precision 0.001 (nm)
> > Last frame 35000 time 100000.000
> > This trajectory file contains coordinate values from 30ns to 100ns. I tried
> to calculate the rmsd with this file (both the trr and xtc file) but the graph
> abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the
> calculation I need the total trajectory from time 0 to time 100ns.I think I am
> missing something.
> Indeed, you're missing your first trajectory.
> You specified -append but if you're changing file names then that won't happen
> and you need to use trjcat afterwards. But since you haven't told us what the
> initial mdrun command was, there's no way to say what's going on for sure.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users