[gmx-users] gold-S simulation

Justin Lemkul jalemkul at vt.edu
Sun Dec 16 23:15:56 CET 2012

On 12/16/12 1:11 PM, francesco oteri wrote:
> Hi fatemeh,
> thank you for the references. Regarding your problem, what does it means
> you don't see any interaction?
> Is it possible it is just a problem of the visualization software. To be
> sure, you could monitor the distance
> between any S atom and the Au atom to which it is supposed to be bound. If
> the distance is stable around
> the equilibrium value you can say that the interaction is still present

In addition, if one is expecting some sort of covalent association, it must be 
defined in the topology.  This will not be true in the case of protein-Au 
interactions unless one makes appropriate entries in specbond.dat, similar to 
heme, or manual addition.  Bonded parameters are useless unless there is a bond :)



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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