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

Justin Lemkul jalemkul at vt.edu
Fri Jul 12 00:46:50 CEST 2013

On 7/11/13 6:41 PM, Neha 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?
> Hi,
> So this is really interesting because I have done the same thing earlier and
> it worked just fine. As in I was trying to do similar non-linear storage and
> it was working fine when eventually it stopped working. Mdrun aborts and
> tells me the input and state checkpoints are not identical. I wish that the
> error was more reproducible or happened consistently because that has not
> been my experience so far.

Then something is inconsistent in your previous protocols or file organization. 
  Either an error will happen, or it won't.  Too many things to guess at here.

> The only reason I don't want to do -noappend is that I will end up with a
> bunch of multiple trajectory files and it would be a pain to sort through
> them. It seems like that might eventually be my only choice.

The analysis tools will complain, anyway.  Whenever a program encounters a 
non-uniform frame interval, it aborts, IIRC.



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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