Re: Strange behavior of NAMD 2.7b1

From: Axel Kohlmeyer (
Date: Thu Jan 14 2010 - 08:53:43 CST

On Thu, Jan 14, 2010 at 7:25 AM, Alexandre Suman de Araujo
<> wrote:
> I think I was not as clear as I desired.
> My question is not about the error which, I know, was discussed many times
> on this list.
> My question is about a possible bug/limitation/problem in any part of NAMD
> code that can be triggered by the choice of prime numbers as pairdistlist
> (and possible as other cut-off parameters), since the impossibility to split
> this kind of number in small ones can bring problems in the parallelization
> process.

first of all, this parameter is a floating point number, i.e. it can be split
any which way you like. your observation of prime vs. non-prime is a
coincidence. furthermore, i suspect you have an unusual view on how
MD is being parallelized in NAMD. the fact that it can or cannot trigger
the reported error condition is due to the fact that this number will affect
how the total _system_ is split into the "patchgrid", but that simply depends
on changing certain parameters, not their absolute value per se.

> As I said, this happened in my simulations and it stopped to crash when I
> exchanged the prime number by any other non-prime number (lower or higher
> than the used prime number).
> As I also said, this can be just a coincidence and I'd like to know if
> anybody else also observed this behavior.

it is rather useless to discuss this, since it is an avoidable error condition.
if you _know_ that your system will be shrinking a lot, you should not wait
until the simulation crashes (or hope that it doesn't) but just run
initially small chunks and restart a few times until the system cell size
doesn't change much anymore.


> Cheers
> --
> Alexandre Suman de Araujo
> Faculdade de Ciências Farmacêuticas de Ribeirão Preto
> Universidade de São Paulo
> Dep. de Física e Química
> Grupo de Física Biológica
> e-mail:
> Phone: +55 (16) 3602-4172

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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