[gmx-users] Re: gold-protein simulation

[fatemeh ramezani]

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?

 
Fatemeh Ramezani