[gmx-users] Charge groups, PME and ions
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 8 19:08:58 CEST 2008
Andreas Kring wrote:
> Hello all.
> I have read the manual and searched the archives, but I am still a
> little confused so here goes:
> I am going to perform an MD simulation of a molecule consisting of 38
> atoms and with a total charge of -4e (water as the solvent). For this
> molecule it is not possible to make charge groups with a total charge of
> zero (or and integer number).
> Is this best solved by using a separate charge group for each atom?...
> and is this allowed since the charge of such a charge group is not zero?
> According to the manual, the charge groups are used to make neighbor
> lists... but these are only important with respect to the computational
> speed as long as PME is used to deal with electrostatic interactions? Or
> have I misunderstood this?
For such a small molecule you can have separate charge groups for each
atom when using PME. Efficiency gains will be minimal when grouping
atoms into charge groups.
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David van der Spoel, PhD, Professor of Biology
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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