[gmx-users] Dividing an MD run

[João Henriques]

tpbconv is the answer for an extension. Choose between -extend or -until,
it's up to you. I like -until, because I'm too lazy to do subtractions :)

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

/J

On Fri, Mar 4, 2016 at 1:27 PM, Guillem Prats Ejarque <
Guillem.Prats.Ejarque at uab.cat> wrote:

> Thanks a lot for your help.
>
> But in my case, the tpr file that I have ran in the first step is not
> useful, because is set to 8 ns, and I want to perform a total run of 20 ns.
> So, to do the next part of the ran, I have to prepare a new tpr of 12 ns
> and run since the last checkpoint? Would be this ok?
>
> grompp -f md_8ns.mdp -c equilib.gro -t equilib.cpt -p topol.top -n
> index.ndx -o md_8ns.tpr
>
> mdrun -nt 16 -v -deffnm md_8ns
>
> grompp -f re_md_12ns.mdp -c md_8ns.gro -t md_8ns.cpt -p topol.top -n
> index.ndx -o re_md_12ns.tpr
>
> mdrun -nt 16 -v -deffnm -cpi md_8ns.cpt md_8ns
>
> Regards,
>
> Guillem
>
> On 3/3/16 6:13 PM, Guillem Prats Ejarque wrote:
> > So, If I have an mdrun running now, but I didn't set in this run an -cpo
> flag, I cannot continue from the last point of this run?
> >
>
> Checkpoint files are written at the interval specified by -cpt.  Unless
> you've
> set that to 0 (or -1, I can't remember) then mdrun will write them
> automatically.  You should see that happen within a few minutes (whatever
> the
> value of -cpt is set to, 15 by default).
>
> -Justin
>
> >
> > On 3/3/16 5:23 PM, Guillem Prats Ejarque wrote:
> >> Hi,
> >>
> >>
> >> I have to do a production MD in an HPC cluster and due to the company's
> policy I have to resubmit the job in the queue everyday. This is probably a
> stupid question, but, to resubmit it starting from the point where I left
> it, do I only have to run the MD again with the output files of the
> previous one, like this?
> >>
> >>
> >> grompp -f remd.mdp -c md.gro -t md.cpt -p topol.top -n index.ndx -o
> remd.tpr
> >>
> >> mdrun ....
> >>
> >>
> >> or should I take into account anything else? Will I obtain the same
> results if I do the dynamic in a single run, or in several steps?
> >>
> >>
> >
> > Once you've created the .tpr file, all you need to do is add -cpi
> -append to
> > your mdrun command to load from the last checkpoint.  Nothing more to
> it.  You
> > can also use -maxh to ensure a clean exit when you hit the wallclock
> limit.  The
> > continuation from the checkpoint is exact.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > 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
> > http://mackerell.umaryland.edu/~jalemkul
> >
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> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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