[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.

> /Andreas
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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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