[gmx-users] Dividing an MD run

[João Henriques]

​Maybe he needs to. Maybe he's comparing or adding replicates to work done
with that version.​ Maybe he uses features that went missing on newer
versions (I know a group doing some more "exotic" work that explicitly
requires 4.0.7). Still, I understand your recommendation and it will be the
"best practice" in most cases.

A nice weekend to everyone!

/J

On Fri, Mar 4, 2016 at 5:39 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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 Correct, though that page is a bit out of date, as tpbconv has been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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