From: Ziemys, Arturas (Arturas.Ziemys_at_uth.tmc.edu)
Date: Wed May 26 2010 - 07:24:54 CDT
Thank you a lot for the insight. I was following tutorial explicitly before too blindly... However, when I have declared just one atom in ref group the performance increased x10 times.
From: heninj_at_gmail.com [heninj_at_gmail.com] On Behalf Of Jérôme Hénin [jhenin_at_ifr88.cnrs-mrs.fr]
Sent: Wednesday, May 26, 2010 4:52 AM
To: Ziemys, Arturas
Subject: Re: namd-l: ABF (NAMD 2.7x) speed ?
[copying this to the mailing list again]
Your "old ABF" and colvars script are not equivalent. In the "old ABF"
script, the reference group abf1 contains a single atom, while in the
colvars script, it is much larger:
colvars: Initializing atom group "ref".
colvars: Atom group "ref" defined, 4432 initialized: total mass = 88831.8.
An atom group containing thousands of atoms is going to be very
detrimental to scaling, because of the additional inter-process
communication involved. There is a warning about this in the user's
guide, but it is not very clear. I'll try to make it clearer and
In this case, you could try and find a smaller set of atoms which has
approximately the same center of mass. Tens of atoms (or maybe a few
hundred) can give reasonable results. Then you can benchmark the old
ABF code using the same atom groups, and tell us about it.
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