I have made SMD simulations in order to separate a Ca2+ ion from its complexation site in the protein, which had charge of about -6 e. Without position constraints in the protein alpha carbons it unfolded in every pull simulation.
2012/12/11 Thomas Schlesier <schl...@uni-mainz.de> > wont happen, since the probability that the ion unbounds itself from the > protein goes down to the cellar. But i hope you get the idea what the > gerneral problem is. If you the pull-dim in each direction this problem > wouldn't occur, since the movement of the ion i -- 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
