[gmx-users] Re: Pulling ion - US

[Leandro Bortot]

     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 <schlesi at 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