[gmx-users] g_saltbr speed

[Justin A. Lemkul]

On 7/12/12 4:51 AM, Kavyashree M wrote:
> Dear Gromacs users,
>
> I was running the saltbridge calculations for a dimeric
> protein simulation using g_saltbr, But its taking very
> long time, almost four days still its not completed.
> Could anyone has suggestion regarding this issue? I am
> using the same system -
> Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
> where i ran MD. Please give some suggestion as to how to
> increase the speed of calculation.
> Command i issued was:
> g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep
>

g_saltbr calculates properties of all possible ionic pairs in the system, so if 
there are many, the calculation might take a long time.  Four days sounds 
ridiculous, and perhaps the program has frozen by exhausting the available memory.

-Justin

-- 
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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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