[gmx-users] g_msd bug

Sławomir Stachura stachura.slawomir at gmail.com
Thu Jul 7 16:15:21 CEST 2011

Thank you for all your answers. It reassures me that the problem I encountered wasn't only a secluded case.
I can also confirm that the -mol options seems to be the one making the most consumption of the resources - without it memory usage has dropped to 20 gb.
And it could be connected to dealing with the PBC, as during my simulation lipids cross very often the boundary between system and its images.


Wiadomość napisana przez Matthew Zwier w dniu 2011-07-07, o godz. 16:02:

> I just experienced this myself.  The problem appeared to manifest
> itself when I was using -mol on a molecule that straddled the box
> wall.  Memory usage was extremely high and the resulting MSD plot did
> not show any linear behavior.  Imaging the trajectory with -pbc nojump
> made g_msd's memory usage drop dramatically and produce a MSD plot
> more like what I would expect -- a linear region on the 10s of ns
> scale bookended by nonlinear regions.  In this latter case, the
> results with and without -mol, though not numerically identical, are
> at least approximately equal.  So, it looks like PBC handling may be
> at fault for one or both of the problems (memory usage and results
> with/without -mol) here.
> Regardless of whether this is a bug or a natural consequence of trying
> to do a MSD calculation on broken molecules, the documentation for
> g_msd implies that g_msd handles periodic boundary conditions
> implicitly; perhaps the documentation should be updated to emphasize
> the (in hindsight, completely logical) fact that molecules need to be
> whole before running g_msd -mol.
> MZ
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Sławomir Stachura
Centre de Biophysique Moléculaire, CNRS
Rue Charles Sadron
45071 Orléans CEDEX 2

E-Mail : slawomir.stachura at cnrs-orleans.fr
E-Mail : stachura.slawomir at gmail.com
URL : http://dirac.cnrs-orleans.fr 

Synchrotron SOLEIL - Division Expériences
Saint Aubin - BP 48
91192 Gif-sur-Yvette CEDEX

Tel : +33 (0)1 69 35 97 51

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