[gmx-users] Can gromacs automatically divided trajectory file into several parts during the simulation process?

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 5 12:59:23 CEST 2010

张春雷 wrote:
> Dear all,
> I am now try to do a long-time all atom simulation. The trajectory file 
> is expected to be larger than 20G bytes. However, my simulation is run 
> on a cluster which only allows me to store 5G bytes file. Therefore, I 
> attempt to divided the trajectory file into several parts but not 
> interrupt the simulation. Does anyone know how to do?

If you move files around or delete them, mdrun should fail with a fatal error. 
Run your simulation in manageable pieces.  The checkpointing capability of 
Gromacs 4 makes extending a simulation trivial.

Otherwise, reduce your output:



> Many thanks!
> Justin Zhang


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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