Louic Vermeer wrote:
Hi gromacs users,
I want to use a topology file for SDS and obviously I am not the first person
doing simulations in SDS. Previous comments on this list suggested using the
prodrg server, but I also read that the partial charges calculated by prodrg
are not always reliable.
What would be the most intelligent thing to do?
1. use the prodrg topology file
2. use the prodrg file, but change the partial charges, using for example the
am1-bcc method. This gives charge-groups that do not sum to a charge of zero
(one group has +0.2 and another one -0.2, which seems quite a lot to me). On
the other hand, the charges in the conjugated SO4 system are more distributed
according to bcc, which seems better to me than the original prodrg topology.
3. hope for someone using this list to send me a "correct" topology file for
sds
http://wiki.gromacs.org/index.php/Parameterization
I would also like to know whether charge-groups are used at all when using
PME. Are they only for cut-off? I did not get that from the manual.
See section 3.4.2 - they are used for neighbour searching, which is
still necessary for L-J interactions. My guess is that they are also
used keeping the direct-space Ewald sum over an integral charge, but I'd
have to read the code to be sure.
Mark
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