[gmx-users] gromacs memory usage

Amit Choubey kgp.amit at gmail.com
Wed Mar 3 02:53:37 CET 2010

> Hi Mark,
> I quoted the memory usage requirements from a presentation by Berk Hess,
> Following is the link to it


> l. In that presentation on pg 27,28 Berk does talk about memory usage but
> then I am not sure if he referred to any other specific thing.
> My system only contains SPC water. I want Berendsen T coupling and Coulomb
> interaction with Reaction Field.
> I just want a rough estimate of how big of a system of water can be
> simulated on our super computers.
> Thank you,
> Amit

On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> ----- Original Message -----
> From: Amit Choubey <kgp.amit at gmail.com>
> Date: Saturday, February 27, 2010 10:17
> Subject: Re: [gmx-users] gromacs memory usage
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Hi Mark,
> > We have few nodes with 64 GB memory and many other with 16 GB of memory.
> I am attempting a simulation of around 100 M atoms.>
> Well, try some smaller systems and work upwards to see if you have a limit
> in practice. 50K atoms can be run in less than 32GB over 64 processors. You
> didn't say whether your simulation system can run on 1 processor... if it
> does, then you can be sure the problem really is related to parallelism.
> > I did find some document which says one need (50bytes)*NATOMS on master
> node, also one needs
> >  (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is
> this true?>
> In general, no. It will vary with the simulation algorithm you're using.
> Quoting such without attributing the source or describing the context is
> next to useless. You also dropped a parenthesis.
> Mark
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