[gmx-users] Extending MD run

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 19 02:00:55 CET 2007


Hi Itamar,

I suppose you could try setting tinit within the .mdp file to a frame that is
present in both the .edr and .trr (similar to the -time suggestion for
tpbconv), and start from that point.  I do believe both the .edr and .trr are
required for an exact restart (at least, if you're using pressure coupling, or
Nose-Hoover temperature coupling, as stated in the wiki).

-Justin

Quoting Itamar Kass <ikass at uq.edu.au>:

> Thank Justin,
>
> Still I am wondering about the grompp option, 'cause this is what I use
> most. You my also say I am invested in this (in CPU time manner).
>
> Itamar
>
> Justin A. Lemkul wrote:
> > Check out:
> >
> > http://wiki.gromacs.org/index.php/Doing_Restarts
> >
> > I think the tpbconv tool might be of more use in your case.  Choose a frame
> that
> > is present in both your .edr and .trr, and specify this time as your
> restart
> > point with the -time option.
> >
> > -Justin
> >
> > Quoting Itamar Kass <ikass at uq.edu.au>:
> >
> >> Hi all,
> >>
> >> In gromacs if you want to extend your run you can do something like
> >>
> >>  > grompp_d -f md.mdp -c MD1.gro -p mol.top -t rom_MD1.trr -e
> >> from_MD1.edr -o for_MD2.tpr
> >>
> >> Now my question is, what happen if the trr file ends at 400ps and the
> >> edr file ends at 399ps? Will it use the trr alone and forget about the
> >> edr file?
> >>
> >> And another one, what it gets from the edr file? After all, the
> >> information it needs is position and velocities from the trr file.
> >>
> >> Best,
> >> Itamar
> >> _______________________________________________
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> >>
> >
> >
> >
> > ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul at vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > ========================================
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================



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