[gmx-users] Re: gold-protein simulation

Justin Lemkul jalemkul at vt.edu
Sun Jan 6 12:27:58 CET 2013

On 1/6/13 5:12 AM, fatemeh ramezani wrote:
> Dear Justin
> What you said is true for bonded parameters, but how about the parameters of the nonbonded file?
> Why Despite  any non-bonded parameters (Sigma, Epsilon) are considered between the gold atom and the other atoms , protein is stretched to the gold cluster  ?
> What is the reason for this closing?Is not it true that when there is no epsilon and Sygma between two atoms, should not be move toward one another?

You should probably have sigma and epsilon values for all interactions.  If you 
don't have any (are they set to zero?) then likely the motion you're seeing is 
just random because there's no other driving force unless charges are involved. 
  In that case, you have basically unscreened Coulombic interactions, which 
likely aren't a very good model for anything, but I've never done any sort of 
gold simulations, so I don't know what people do in that case.



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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