[gmx-users] Problem control output for checkpoint file

Justin Lemkul jalemkul at vt.edu
Tue May 19 15:40:08 CEST 2015

On 5/19/15 9:24 AM, Vy Phan wrote:
> Dear Gromacs Users!
> I am a beginner. I am looking for the command line corresponding with
> nstcheckpoint (control the output of the checkpoint file) in the Gomacs
> 5.0.4 but I coudn't find. And when I check the log file, I also can not
> recognize what command line which controls cpt file.

Read the mdrun help information:

  -cpt   <real>   (15)       Checkpoint interval (minutes)

> The second question, when I run energy minimization I got only one frame, I
> try to reduce the frequency saving the coordinates but I still get the same
> result (it look the control output did not working ). I want to save more
> frame to see what happen in the energy minimization step . Can some one
> help me?

If EM finishes in one step, either (1) the structure was already minimized or 
(2) EM failed.  The .log file will tell you happened.

> The third question, I want to generate only the xtc file (I do not want to
> generate the trr file). What command I need to use for Gromacs 5.0.4 ? (I
> know the command constxtcout when I search on google, but I can not find
> the information for it on gromacs manual 5.0.4)

nstxout-compressed is the current keyword.  Suppress the .trr by setting 
nstxout, nstvout, and nstfout to zero.

Make sure you do some basic tutorial material; these elements are all covered by 
most, if not all, of them.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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