[gmx-users] g_saltbr speed

[Kavyashree M]

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
so.

Thank you
kavya

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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