Re: AW: time per step during GPU-accelerated Implicit Solvent calculations

From: Thomas Albers (talbers_at_binghamton.edu)
Date: Wed Nov 18 2015 - 08:38:07 CST

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Hi Jim,

thanks for this hint. With the center-of-gravity restrained to its
initial position time/step remains very much constant. Adjusting the
load balancing interval, as Norman suggested, didn't help.

Could NAMD print a warning message when the number of atoms per patch
becomes too unequal amongst all the patches? Just a suggestion for
upcoming version 2,11.

Regards,
Thomas

> My theory is that due to the lack of periodic boundary conditions your
> protein has drifted outside of the initial patch grid and is now entirely
> in a single patch so the parallel decomposition is ineffective. If you
> restrain the molecule in some way that should limit the performance loss.

> Implicit solvent in NAMD was originally intended for use in fitting to
> electron densities for which this isn't an issue.

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