[gmx-users] gromacs memory usage

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 3 05:06:22 CET 2010

On 3/03/2010 12:53 PM, Amit Choubey wrote:
>     Hi Mark,
>     I quoted the memory usage requirements from a presentation by Berk
>     Hess, Following is the link to it
> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
>     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.

Try increasingly large systems until it runs out of memory. There's your 


> On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>> wrote:
>     ----- Original Message -----
>     From: Amit Choubey <kgp.amit at gmail.com <mailto: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
>     <mailto: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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