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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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