[gmx-developers] strange forces in MD of protein-lipid system

Rainer Böckmann rainer at bioinformatik.uni-saarland.de
Fri Sep 22 17:33:37 CEST 2006

Dear Developers,

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.


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 mailing list