[gmx-users] RE: Is non-linear data output/storage possible?

Justin Lemkul jalemkul at vt.edu
Mon Jul 15 17:54:17 CEST 2013

On 7/15/13 11:48 AM, Neha wrote:
> Justin Lemkul wrote
>> The .cpt file stores information related to output frequency.  The
>> existing.cpt
>> file designates output every X steps, while the new .tpr file specifies
>> output
>> every Y steps, and X != Y, so mdrun complains.  I'm assuming mdrun aborts
>> at
>> that point?  Have you tried with -noappend?
> The information on the extending simulations page does not seem to agree
> with what you just said above. It says :
> If you wish/need to change .mdp file options, then either
> grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt
> mdrun -s new.tpr
> or
> grompp -f new.mdp -c old.tpr -o new.tpr
> mdrun -s new.tpr -cpi old.cpt
> should work.
> I am simply changing the mdp file options so the difference in output
> frequency shouldn't actually cause mdrun to abort.

That section of the wiki was written years ago, when the default behavior of 
mdrun was to not append files unless specifically requested.  Now that mdrun 
does append by default (as of version 4.5), you probably have to add -noappend. 
  If that works, then I'm happy to update the wiki, but since what you're trying 
to do is not common, there was no compelling need to update the wiki to reflect 
the difference.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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