[gmx-developers] artificial forces in MD of lipid bilayer system

David Bostick dbostick at scripps.edu
Thu Oct 5 18:48:16 CEST 2006

Are you sure that this extraction is due to artificial forces?  Changing 
the number of processors will produce small numerical changes in the 
integration, which can in turn, affect the outcome of a simulation. When 
simulating bilayers, I have seen many things happen ... from extraction of 
lipids ... to lipids finding their way into the hydrophobic interior (head 
group and all) ... to spontaneous formation of water wires and pores. This 
especially can happen when an initial configuration has a few 
instabilities in it. I see no reason why such an event could not even 
occur from time to time in a real bilayer.

I understand that one cannot rule out some form of artifact in gmx, but it 
might be worth considering that, based on your description of the event, 
your system may be behaving normally.


David Bostick
The Scripps Research Institute
Dept. of Molecular Biology, TPC 6 
10550 N. Torrey Pines Rd.
La Jolla, CA 92037

Phone: 858-784-9614
Fax:   858-784-8688
Email: dbostick at scripps.edu
Web:   http://www.scripps.edu/~dbostick

On Thu, 5 Oct 2006, [ISO-8859-1] Rainer Böckmann wrote:

> Dear Developers:
> we reproduced the extraction of a lipid out of a bilayer reported two weeks 
> ago for a mixed system, now for a pure POPC lipid bilayer, using the Berger 
> forcefield (gromacs 3.3.1, x86_64).
> A lipid is extracted within 100ps when using 8 procs, the bilayer stays 
> intact on 4 procs and also when manually distributing the atoms across the 
> nodes with the -load option of grompp. A bugzilla with all necessary files is 
> submitted.
> Best wishes,
> Rainer
> -- 
> __________________________________________________________
> Dr. Rainer Böckmann
> Theoretical & Computational Membrane Biology
> Center for Bioinformatics Saar
> Universität des Saarlandes
> Gebäude C7.1 (17.1), EG
> D-66041 Saarbrücken, Germany
> Phone: ++49 +681 302-64169  FAX: ++49 +681 302-64180
> E-Mail: rainer at bioinformatik.uni-saarland.de
> http://www.bioinf.uni-sb.de/RB/
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