Re: metadynamics simulations slow down and down

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sun Sep 26 2010 - 05:47:28 CDT

Hi,

Did you disable the useGrids option? This sounds like the slowdown
that happens when the number of stored hill potentials become large,
and summing them becomes increasingly expensive. The grid-based
version should solve this - although it is only available for scalar
variables.

Cheers,
Jerome

2010/9/26 OiniL <noinil_at_gmail.com>:
> Dear Namd Users:
>
> I'm using metadynamics to simulate the folding of a protein with NAMD.
>
> After several hours... Running speed got more and more slower.
>
> The speed at the beginning was
> "CPU: 2.30465, 0.00455531/step Wall: 2.30378, 0.00455352/step,"
> but 10 hours later, it's
> "CPU: 165525, 0.0223486/step Wall: 165964, 0.0223666/step,"
>
> about 1/5 the speed at the beginning.
>
> I tested another equilibrium run with the conf.file totally same as the
> metadynamics file except the part of colvars, and this time the speed looks
> fast and stable.
>
> Is there anybody else have had a same experience?
> How can I check what is wrong?
>
> Any help or hint is appreciated
>
> Best regards!
>
> Cheng TAN
> PhD student of Biophysics Dept.
>
> Nanjing University
>
> --
> ---------------------------------------------------------------------------------
> ×£
> ½¡¿µ¿ìÀÖ
>
> Ì·Ø©
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:09 CST