[gmx-users] continuation of simulation

[David van der Spoel]

On Mon, 2004-11-22 at 20:16 -0600, Dinesh Pinisetty wrote:
> 
> 
> 
> Hello everyone,
>           As Dr.David said I used an option -until 10000 but still when the
> simulation is started GROMACS shows the time as 9662.Why is it not able to
> show exactly 10000.
>   I am extending the simulation from 4ns to 10ns.
Use gmxcheck to see what's in your files.
> Thanking you,
> Dinesh.
> 
> 
> 
> From:gmx-users-bounces at gromacs.org on 11/21/2004 10:00 AM CET
> 
> 
> Sent by: gmx-users-bounces at gromacs.org
> 
> Please respond to Discussion list for GROMACS users <gmx-users at gromacs.org>
> 
> 
> 
> To:   Discussion list for GROMACS users <gmx-users at gromacs.org>
> cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)
> 
> Subject:    Re: [gmx-users] continuation of simulation
> 
> 
> 
> On Sat, 2004-11-20 at 19:43 -0600, Dinesh Pinisetty wrote:
> >
> >
> >
> > Hi all,
> >          I have run a simulation for 4ns.I wanted to extend it to 10ns.So
> I
> > used,
> > tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr -extend 6000
> > When I used this it displayed 4685000(steps) and 9370 ps.Shouldn't it
> show
> > as 10000.Now by mistake at step 3747100 I killed the job.Now again I
> > extended it by using the same command which I mentioned earlier by
> 2000.Now
> > it displays as 5655000 and 11370 what does this mean.
> your first simulation did not go to 4 ns but only to 3370
> the second time around you added 2000 to 9370.
> 
> You can also use the -until 10000 option.
> 
> > Thanking you,
> > Dinesh....
> >
> >
> >
> >
> >
> >
> >
> > From:gmx-users-bounces at gromacs.org on 11/09/2004 08:44 AM ZE8
> >
> >
> > Sent by: gmx-users-bounces at gromacs.org
> >
> > Please respond to Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> >
> >
> >
> > To:   Discussion list for GROMACS users <gmx-users at gromacs.org>
> > cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)
> >
> > Subject:    Re: [gmx-users] continuation of simulation
> >
> >
> >
> > Dear Dinesh,
> >
> > Just to add to what Ran has said:
> >
> > tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr -extend 6000
> >
> > The "-e ener.edr" only exists in GROMACS 3.2.x and helps preserve
> accuracy
> > of runs under temperature/pressure coupling.
> >
> > Use tpxout.tpr in place of topol.tpr in your MD run.
> >
> > However, note that tpxout.tpr preserves whatever settings you have used
> for
> > topol.tpr, including the number of processors to be used for a parallel
> > run.
> >
> >
> > regards,
> > Choon-Peng
> >
> > On 11/9/04 7:49 AM, "Ran Friedman" <ran at hemi.tau.ac.il> wrote:
> >
> > > Dear Dinesh,
> > >
> > > use tpbconv to make a new input file for your run.
> > >
> > > Ran.
> > >
> > > Dinesh Pinisetty wrote:
> > >
> > >>
> > >>
> > >> Dear users,
> > >>            I have simulated a system for 4ns.Now I want to continue
> that
> > >> till 10 ns.How to start from where I left and rerun the simulation for
> > >> extended times.
> > >> Thanking you,
> > >> Dinesh.
> > >>
> > >> _______________________________________________
> > >> gmx-users mailing list
> > >> gmx-users at gromacs.org
> > >> http://www.gromacs.org/mailman/listinfo/gmx-users
> > >> Please don't post (un)subscribe requests to the list. Use the
> > >> www interface or send it to gmx-users-request at gromacs.org.
> > >>
> > >> +++++++++++++++++++++++++++++++++++++++++++
> > >> This Mail Was Scanned By Mail-seCure System
> > >> at the Tel-Aviv University CC.
> > >>
> > >>
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++