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.
________________________________________________________________________
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
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