[gmx-users] g_saltbr speed

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 12 12:09:32 CEST 2012

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


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