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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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