Re: [AMBER] running sgld in explicit solvent

From: David A Case <>
Date: Thu, 16 Jul 2015 08:48:15 -0400

On Thu, Jul 16, 2015, Asmita Gupta wrote:
> I have some basic questions regarding running SGLD simulation in amber14.
> The total no of atoms in my system are 359214 (including waters), but i am
> printing only 1-864 atoms in the trajec file..However, a run of 1ns takes
> approx 72-75 hrs to finish. (40 xeon cores , E52680)

Which program are you using? How many nodes do you have, and what is the
nature of the interconnect between nodes?

> 1.) In explicit solvent conditions, does the guiding force is limited to
> only solute or is applied to solvent molecules also? Is this why 1ns run is
> taking this much time?

SGLD is probably not the culprit here. You can easily compare timings for a
short run with and without SGLD to compare timings.

> 2.) Can i use something like isgsta=1 and isgend=864 to specify the range
> on which guiding force should be applied?

You can try this. I doubt that it will affect the timings, but you can easily
enough experiment to find out. I'd suggest trying some test simulations with
many fewer waters, to get a feeling for what is affecting your performance.
Don't forget to try fewer cores as well.


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Received on Thu Jul 16 2015 - 06:00:05 PDT
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