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

Rainer Böckmann rainer at bioinformatik.uni-saarland.de
Thu Oct 5 20:13:38 CEST 2006

Dear David,

you can certainly sometimes observe strange behaviour of lipid bilayers. The
bilayer used here was pre-equilibrated for about 200ns with gromacs 
3.2.1, thus
we considered the initial structure equilibrated.

However, if you exchange two lipids in the initial pdb/gro (one of them being
extracted in the simulation)and restart the simulation the new lipid at the
position of the before extracted lipid will leave the bilayer, again on the
timescale of 100ps. Obviously there are strange forces acting on atoms at
specific positions in the pdb-file. Everything is fine when using 4 procs or
manually distributing the atoms using the load option of grompp.


Quoting David Bostick <dbostick at scripps.edu>:

> 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.
> Best,
> David
> =======================================
> 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 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

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