[gmx-users] mdrun -nsteps

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 17 13:49:00 CET 2015


The second call to mdrun will run 10000 steps if it can. Whether that is a
continuation or not depends what checkpoint mdrun finds, etc.

gmx mdrun -h says

"-nsteps Run this number of steps, overrides .mdp option"

This is true, from the point of view of the next MD simulation part, which
is what mdrun does. That this part is just one piece of a bigger picture
isn't something mdrun needs to help you manage, I think.

Using the word "append" would be ambiguous, because gmx mdrun -append
refers to running some number of steps and concatenating the output files
(or not, with -noappend). "Continue" doesn't fully work either, because it
implies the existence of a previous simulation part.

The main alternative would be defining -nsteps as "do this total number of
steps, starting from the checkpoint (if any)." This isn't very usable
unless you know for sure what is in your checkpoint. The current meaning
for -nsteps means that it is easy to write a job submission script e.g. for
2 hours doing 50,000 more steps - which is awkward otherwise.



On Tue, Feb 17, 2015 at 12:10 PM, Sabine Reisser <sabine.reisser at kit.edu>

> Hi,
> just to be sure: is it intended, that the -nsteps option in mdrun (which
> is a great feature in general!) actually appends the given number of steps
> rather than overriding the mdp option?
> This is what I do:
> - grompp with mdp file with 5000 steps
> - mdrun
> - mdrun -nsteps 10000 steps
> The second mdrun runs until 15000 steps, not 10000 steps. Is this
> intended? If yes, the option description is somewhat misleading.
> Cheers
> Sabine
> --
> Dipl. Phys. Sabine Reißer
> Karlsruhe Institute of Technology (KIT)
> Institute of Physical Chemistry
> Phone +49 (0) 721 / 608-45070
> --
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list