Mark Abraham wrote:
[EMAIL PROTECTED] wrote:
Hello,
I'm interested in running a simulation in which the box will be
divided in to two different dielectric constants separated at a plane.
Is it possible to do that in Gromacs?
Possible, yes. However it is not implemented, and it is not a trivial
change to do so.
If you do that (and implement a position dependent epsilon_r that is not
1) your system will most likely explode. Using epsilon_r different from
1 means that the weighting between Coulomb and Van der Waals forces will
be different. For e.g. water e_r > 1 will make the system explode, e_r <
1 will make it implode. Your choice.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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