[gmx-users] Restarting mdrun

[Chandan Choudhury]

Thanks Lum !!!
I had already used the suggestion you mentioned. But my problem is somewhat
different. You can go through my previous mail, for more information.

Thanks.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Tue, Feb 16, 2010 at 11:42 PM, Lum Nforbi <lumngwegia at gmail.com> wrote:

> Hi Chadan,
>
>     I have used the two commands below to CONTINUE a run and they worked
> fine for me. I am also using gromacs-4.0.5.
>
> tpbconv -s wfullmdrun_extend2.tpr -extend 2000 -o wfullmdrun_extend3.tpr
> mdrun -s wfullmdrun_extend3.tpr -o wfullmdrun_traj.trr -e
> wfullmdrun_ener.edr -g md.log -cpi state_prev.cpt -append &
>
> The first command includes the amount of time by which you want to extend
> your run.
> The second one just appends the results to your existing files. In this
> second command, you are using the new .tpr file you created in the first
> command. Use the state.cpt file instead of the state_prev.cpt file in order
> to avoid losing time.
>
> Hope this helps.
>
> Lum
>
>
>    On 17/02/10 02:52, Chandan Choudhury wrote:
> > Hello gmxusers !!!
> > I want to continue my simulation, from where the point where it stopped.
> > The gmxcheck on .trr and cpt files are as:
> >
> > $gmxcheck -f state.cpt
> >
> > Checking file state.cpt
> >
> > # Atoms  186864
> > Last frame         -1 time 9362.500
> >
> >
> > Item        #frames Timestep (ps)
> > Step             1
> > Time             1
> > Lambda           1
> > Coords           1
> > Velocities       1
> > Forces           0
> > Box              1
> >
> > $gmxcheck -f 5-10.trr
> >
> > Checking file 5-10.trr
> > trn version: GMX_trn_file (single precision)
> > Reading frame       0 time 5169.500
> > # Atoms  186864
> > Reading frame    8000 time 9169.500
> >
> >
> > Item        #frames Timestep (ps)
> > Step          8395    0.5
> > Time          8395    0.5
> > Lambda        8395    0.5
> > Coords        8395    0.5
> > Velocities    8395    0.5
> > Forces           0
> > Box           8395    0.5
> >
> >
> > There is a mismatch of time in both the outputs.
> >
> > The date of modification of both the files as shown are:
> >
> > Feb 15 19:55 state.cpt
> >
> > $date -r 5-10.trr
> > Mon Feb 15 19:59:56 IST 2010
> >
> > The cpt file shows time greater than the trr file. But the time of
> > modification of cpt file is less than trr file.
>
> If the simulation stopped catastrophically, then the timestamp could
> easily differ, especially if the .cpt is opened, written to and closed
> periodically, and the .trr is open continuously.
>
> > Cannot understand the,
> > how to restart the mdrun. And the size of the trr file is 36GB. Can I
> > use the append flag in mdrun for gmx 4.0.5.
>
> Search the webpage for suggestions.
>
> Mark
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100217/96bd8633/attachment.html>