[gmx-users] Charge groups, PME and ions [SOLVED]
akring at fys.ku.dk
Wed Oct 8 21:56:08 CEST 2008
David van der Spoel wrote:
> 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.
Great! Thanks a lot.
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