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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
