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

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

-Justin

> Many thanks!
> 
> Justin Zhang
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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