[gmx-users] Extending MD run

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 19 02:37:01 CET 2007

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.

> I suppose it would be just as easy to remove any reference to tinit in the .mdp,
> but in any case I'm curious.


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