Re: [gmx-users] Re: gold-protein simulation

2013-01-06 Thread Justin Lemkul
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 t

[gmx-users] Re: gold-protein simulation

2013-01-06 Thread fatemeh ramezani
Dear Justin What you said is true for bonded parameters, but how about the parameters of the nonbonded file? Why DespiteĀ  any non-bonded parameters (Sigma, Epsilon) are considered between the gold atom and the other atomsĀ , protein is stretched to the gold cluster ? What is the reason for this