AMBER Archive (2009)
Subject: Re: [AMBER] A good way to use an Amber force field with NAMD?
From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Tue Mar 03 2009 - 20:55:56 CST
Actually, I like this idea. Regarding scaling, though: do you know how
well PMEMD scales on over 1024 processors compared to NAMD? I keep
hearing that NAMD is considerably faster at these cpu numbers..
If the scaling is comparable, I'd certainly try to do a local install
(and could use your help in that case).
Ross Walker wrote:
>> to answer your question about the requirement: we are trying to get some
>> supercomputer time, and they only have NAMD installed. In any event,
>> it's not our choice.
> Just a quick question. Why not just install AMBER yourself. It builds on
> every supercomputer I have ever used without issues. You can install it in
> your home directory as well.
> To be honest even if I planned to use NAMD I'd do this. It can be pretty
> brave to use the supercomputer center installed version unless you
> implicitly trust the person who installed it.
> If you let me know what machine it is I can probably install AMBER for you
> (or give you a suitable config file to use).
> All the best
> |\oss Walker
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
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