[gmx-users] Re Can GROMACs use multiple van der Waals potentials and multiple van der Waals potential cutoffs?

[David van der Spoel]

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se