On 2013-03-15 19:27, Jeff Woodford wrote:
Hi all,
I am attempting to simulate a system that has strong ionic character so I would
like to treat the electrostatics and van der Waals interactions separately.
For example I would like to include all pairs of atoms in the electrostatics
calculation but I would like to exclude 1-2 and 1-3 neighbors in the van der
Waals calculation. Is this possible to do in GROMACS? If so, how might this
be accomplished? Thanks in advance for your help.
Jeff Woodford
Assistant Professor of Chemistry
Missouri Western State University
In a molecular system you can do this by adding the 1-2 and 1-3
interactions as pairs, assuming the list of interactions is fixed, like
in a crystal. Then you can make the LJ parameters different from the
default and scale the charges down. You probably want to use PME for
electrostatics. Check the manual!
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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