[gmx-users] problem with the max number of atom in charge group

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 14 08:36:56 CEST 2007

Nicolas Sapay wrote:
> Hello everybody,
> I'm trying to use a DPPC bilayers with charges from the Jacob Sonne et 
> al. study (Biophys J., 2007). The problem is that the authors have 
> defined a single group for the whole DPPC molecule. This allow them to 
> define new accurate charge for the head group atoms and the first atoms 
> of the acyl chains. It is a problem with Gromacs which tolerate only 32 
> atoms per group (When I try to minimize my system, I've got the error : 
> Max #atoms in a charge group...). In Gromacs, is it possible to defined 
> groups with a net charge different form an integer, like 0.026042? Would 
> it be a problem if I use PME? Note that the net charge of the molecule 
> is still zero, of course.
> Thanks
> Nicolas
If you use PME than this is perfectly fine. You do not want charge 
groups larger than 3-4 atoms because the charge group is also used for 
neighborsearching, that means LJ interactions are between whole charge 
groups as well.

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://folding.bmc.uu.se

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