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

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 22 18:20:32 CEST 2006

On Fri, 22 Sep 2006, Rainer Böckmann wrote:

>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.

are you sure this is the case? is it not pbc?

otherwise, is it not due to an error in the topology? there is recent 
bugzilla on strange effects due to the topology.

in addition, do you have the pme_order bug fixed, for pme_order != 4?

if you think this is a bug, submit a bugzilla.


David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-developers mailing list