Re: questions about user defined potential in NAMD

From: Axel Kohlmeyer (
Date: Tue Dec 14 2010 - 04:10:05 CST

On Mon, Dec 13, 2010 at 4:48 PM, Chen, Zhihong (chenz2)
<> wrote:
> Hi  all,
>  i want to simulate a protein-membrane system with some ions in it.  I need to specify the interaction potential between the ion and protien. I know in Gromacs we can use a user-defined table to do this job. Can this be done in namd? could anysome send me some instructions?

is there any special functional form needed for that potential?

most standard ions are just represented by their charge and
a set of lennard jones parameters, just like any other atom types.
so that using tabulated potentials are not required (also in gromacs).

in some special cases (some divalent cations), for the CHARMM
force field, the NBFIX section is used to override the normal
atom type mixing rules for lj parameters for an improved (though
limited to pairwise additive terms) representation.


> regards,
> jackie

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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