[gmx-users] Dividing an MD run

[Mark Abraham]

Hi,

The log file reports what it's doing and hopefully why... But nobody should
be starting new work with 4.5.x or 4.6.x. They are older, slower, have
fewer features, have more bugs, and are out of maintenance...

Mark

On Fri, 4 Mar 2016 17:34 João Henriques <joao.henriques.32353 at gmail.com>
wrote:

> Hmmm, that's odd. I don't see why though. Maybe Justin or any other gromacs
> guru can help you spot the problem.
>
> P.S.: What did the std out from tpbconv say?
>
> /J
>
> On Fri, Mar 4, 2016 at 4:46 PM, Guillem Prats Ejarque <
> Guillem.Prats.Ejarque at uab.cat> wrote:
>
> > Actually, I'm using GROMACS 4.5.5, so, it is ok for me. I generated the
> > new tpr file with 20 ns
> >
> > tpbconv -s md_8ns.tpr -until 20000 -o md_12ns.tpr
> >
> > and I ran it since the last md checkpoint:
> >
> > mdrun -nt 8 -s md_12ns.tpr -cpi md_8ns.cpt -v
> >
> > But, it runs 20 ns from 0, not 12 ns from 8, as it should do. What am I
> > doing wrong?
> >
> >
> > On 3/4/16 8:32 AM, Jo?o Henriques wrote:
> > > 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
> > >
> >
> > Correct, though that page is a bit out of date, as tpbconv has been
> renamed
> > convert-tpr.
> >
> > -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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