[gmx-users] Question about gold-S simulation

Justin Lemkul jalemkul at vt.edu
Thu Jan 3 22:59:51 CET 2013

On 1/3/13 3:49 PM, hyunjink at andrew.cmu.edu wrote:
> Hi,
> I saw Fatemeh's and others' posts regarding gold and S FF parameters.
> I have a few questions regarding this:
> 1. The vdW parameters for Au changed according to interaction atoms such
> as C, H, N, S, etc.
> However, I wonder, if the system includes both S and N, which interact
> with Au, then which parameter should I use for Au, one for Au-N or one for
> Au-S.

LJ parameters listed in [atomtypes] in ffnonbonded.itp are used in conjunction 
with the combination rules of the force field to determine these interactions. 
If interactions change depending upon the atoms involved, one can specify 
[nonbond_params] for each interaction pair that supersede the combination rules 
for those atom pairs.  That way, the parameters for e.g. S can be different when 
interacting with different atoms.

I can't comment on points 2 and 3.


> 2. Can you send me papers you obtained the FF parameters for Au?
> 3. The charge of Au is zero?
> Thanks in advance.
> Hyunjin.


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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