[gmx-users] g_saltbr speed

Kavyashree M hmkvsri at gmail.com
Fri Jul 13 18:05:32 CEST 2012

Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will
that be insufficient? I have previously run other analysis which used to take
huge memory, for eg. covariance analysis, in a system with much lesser memory
even though CPU usage was low the job used to finish. But in this case its not

Thank you

On Fri, Jul 13, 2012 at 9:22 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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