回复： [gmx-users] Re Can GROMACs use multiple van der Waals potentials and multiple van der Waals potential cutoffs?
cynthiahong1983 at yahoo.com.cn
Wed Mar 31 23:31:54 CEST 2010
Thanks. But I've read the manual. It seems not solving it. The two potentials in my system are of totally different function forms. They do not just differ in the parameters. What troubles me is GROMACS seems not to be able to support two function forms simultaneously for van der Waals interactions.
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
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
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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