[gmx-users] continuation of simulation

[Dinesh Pinisetty]

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.
Thanking you,
Dinesh.



From:gmx-users-bounces at gromacs.org on 11/21/2004 10:00 AM CET


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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.
> >>
> >> _______________________________________________
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--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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