[gmx-users] Extending MD run

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 19 02:22:51 CET 2007

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 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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