[gmx-developers] Re: strange forces in MD of protein-lipid system
rainer at bioinformatik.uni-saarland.de
Sat Sep 23 17:03:28 CEST 2006
David van der Spoel wrote:
>On Fri, 22 Sep 2006, Rainer Böckmann wrote:
>>we found strange forces acting on one lipid in a mixed protein-lipid
>>system (~24k) running on 8 processors (3.3.1, PME), resulting in this
>>lipid leaving the membrane on the timescale of 10-100ps (stable
>>simulation). This force acts only on atoms in a specific position of the
>>pdb-file, i.e. exchanging two lipids will result in a different lipid
>>leaving the membrane. Also, restart on a different number of processors
>>avoids this artefact. If required we can support the respective tpr-files.
>are you sure this is the case? is it not pbc?
yes, no PBC effect. One lipid is smoothly extracted from of the
membrane, the results are reproducible with e.g. different initial
>otherwise, is it not due to an error in the topology? there is recent
>bugzilla on strange effects due to the topology.
could not find any bug in the topology
>in addition, do you have the pme_order bug fixed, for pme_order != 4?
we used pme_order=4 together with gromacs 3.3.1
>if you think this is a bug, submit a bugzilla.
we'll submit a bugzilla next week.
Thanks & best wishes,
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
More information about the gromacs.org_gmx-developers