[gmx-users] g_saltbr speed

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 13 17:52:29 CEST 2012

On 7/13/12 11:50 AM, Kavyashree M wrote:
> Dear users,
> Its the continuation of the question I asked yesterday, Inorder to reduce
> the memory usage during g_saltbr calculations i got the trajectory of only
> protein, and tpr file without water and was able to successfully run it. But
> unfortunately this again got stopped at 36ns as it had stopped when i was
> using the whole trajectory. I tried with -dt 2, still the same problem exists.
> Kindly suggest a way out of this situation.

How long is the trajectory?  How many frames?  What is the size of the file on 
disk?  It sounds to me like you're simply exhausting available memory, so the 
only advice is in the link I posted before - use fewer frames or use a machine 
that has more memory to do the analysis.



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


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