[gmx-users] Extending MD run

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 19 02:55:58 CET 2007

Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:

> Justin A. Lemkul wrote:
> > Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
> >
> >> Itamar Kass wrote:
> >>> 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).
> >> You being cryptic doesn't serve your purpose of getting useful free help
> >> :-)
> >>
> >> Justin's advice was correct but incomplete, in that grompp also has a
> >> -time option you can use. The advice on the URL he provided will answer
> >> both this and your other questions, as would reading the GROMACS manual
> >> and/or man page :-)
> >
> > Thanks for pointing that out Mark, but I am wondering if you (or anyone
> else out
> > there) might be able to clear up a little confusion I have (and hence the
> reason
> > I have always used tpbconv if my .edr and .trr don't match up for whatever
> > reason).  Does the tinit option in the .mdp file override the -time
> argument,
> > in the same way that gen_vel = yes would override the velocity input from
> the
> > .trr?  The manual and online documentation don't seem to give me a clear
> answer
> > to this question.
> I haven't tested that one... tinit overrides the time of the last
> useable frame if you don't supply -time, so I'd have to suppose it works
> the same way if the frame is specified with -time. If this were not
> true, then tinit would be constrained to be a time in the supplied
> trajectory. This kind of thing would be easy to check with some quick
> changes to .mdp and/or command line and comparison of the output .tpr
> with gmxcheck -s1 -s2.
> If you do this, please report what you see and I'll update the wiki page.

>From a quick test case, it appears that -time does not override what is
specified in the .mdp file.  For example, if tinit = 1000 in the .mdp file, but
then I issue:

$ grompp -f test.mdp -c conf.gro -p topol.top -t traj_1ns.trr -e ener_1ns.edr
-time 500 -o test.tpr

The output .tpr file starts at 1000 ps.  So I suppose one would have to nix the
tinit line in the .mdp in order to use -time.


> > I suppose it would be just as easy to remove any reference to tinit in the
> .mdp,
> > but in any case I'm curious.
> Mark
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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