[gmx-users] Split Trajectory file into parts

Justin Lemkul jalemkul at vt.edu
Sat Aug 29 16:22:47 CEST 2015

On 8/29/15 9:10 AM, Johnny Lu wrote:
> Dear Users,
> Simulation writes to a Lustre file system (a distributed file system made
> of many hard drives).
> About 100 Gb was written in 1 hrs. After a while, gromacs 5.1 says it can't
> write the trajectory file.
> The file system still has lots of space. Not sure if that was because one
> of the many hard drives filled up.
> Is it possible to ask gromacs to automatically split the trajectory files
> into parts?


> Or, I have to write a shell script to make gromacs restart the simulation
> every 15 minutes?

Yes.  Or, heed what grompp tells you about how much data will be generated and 
simply construct a very trivial loop to execute mdrun for N steps, invoke 
convert-tpr, mdrun -cpi -noappend, etc.



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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