Re: [AMBER] RAM requirements

From: David A Case <>
Date: Wed, 1 Jun 2011 13:29:51 -0400

On Wed, Jun 01, 2011, Dmitry Osolodkin wrote:
> I've tried to make a solvated protein in tleap with the command
> "solvatebox M TIP3PBOX 275" to start with rather simple test system. It
> used 8 Gb RAM, then 7.5 Gb swap and hanged. It probably means that
> solvatebox routine memory usage is not optimal.

This appears(?) to be about 16 million atoms or so, which is way beyond the
design of the Amber codes and (probably) the experience of anyone. I
understand that you are looking towards a new generation of computers, but you
are going to have to learn a lot about the innards of the Amber code, and be
willing to experiment, in order to have much hope of getting anywhere. The
mailing list is not going to be of much help, I fear.

The Amber prmtop file allows you to define your own formats, so that (in
principle) very large numbers of atoms, bonds, dihedrals, etc. can be
represented. But I don't know anyone who has made use of this, and you will
almost certainly be writing some of your own code.

By all means, try loading a humongous pdb file from Gromacs into either tleap
or sleap, and see what happens.


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Received on Wed Jun 01 2011 - 11:00:02 PDT
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