On 2010-03-31 21.53, hong bingbing wrote:
Thanks, David.
Let me simplify my system. It includes A and B molecules. The van der
Waals interaction between A's is, e.g. U1(r) = -1/r cutted off at r =
r_A ; and for B: U2(r) = -1/r^2, cut off at r = r_B.
I don't know how to handle with two potentials and two cutoffs
simultaneously.
Read manual and online instructions about tabulated potentials in
gromacs. You have to specify files for each interaction pair, that is
AA, AB, BB, then simulate with cutoff max(r_A,r_B). Make sure the
potentials are continuous and smooth to at least the cutoff.
-----------------------------------
Dear all,
I'm trying to simulate multiple phases in one system. Each phase has
distinct van der Waals potential form and different
cutoffs from the rest. Unfortunately, I found only one van der Waals
potential and one cutoff can be defined in .mdp file of one run. Did I
miss some features of GROMACS? Have you encountered this problem before
and could you lend a help?
Thank you
Cynthia
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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