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
--
========================================
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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