[gmx-users] Load imbalance and Y size error

Berk Hess gmx3 at hotmail.com
Thu Oct 8 16:20:13 CEST 2009


I am very hesitant to put in such checks.
In most cases they would not be necessary.
I a few cases it would help a user that does not know exactly would he/she is doing.
But I don't like to make life harder for people who do know what they are doing
and are simulating systems that are not the "standard" atomistic biomolecular simulations.

I said this before this week in another thread:
having grompp stop (which it does now with one warning) when you know what you
are doing is EXTREMELY annoying, already on the command line, but even more in scripts.
This has happened to me when someone had added some absolute range checks
on some mdp parameter, which would always work for atomistic biomolecular simulations,
but not for, for instance, dimensionless simulations.


> Date: Thu, 8 Oct 2009 23:46:03 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Load imbalance and Y size error
> Berk Hess wrote:
> > Hi,
> > 
> > Do not "randomly" change the fourierspacing.
> > Are you really using PME in vacuum?
> > 
> > The box size can only change if you have pressure coupling turned on,
> > which should, obviously, should not do in vacuum.
> This suggests adding a warning about pressure coupling when the atomic 
> distribution is strongly non-homogeneous... but what's an easy test for 
> that? Is a 3x3x3 grid search in grompp out of the question? More than 
> 50% variation in atom number density per grid volume would probably pick 
> up vacuum simulations but not show false-positive membrane simulations.
> Mark
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