Thank you all! On Tue, Dec 11, 2012 at 12:54 PM, Leandro Bortot <leandro....@gmail.com> wrote: > 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.
I applied position restarints of terminals (it is helix) heavy atoms and used force constant of 2000 and pulling rate of 0.01. Then the force vs time clearly shows the breaking point and helix does not lossed its secondary structure. Steven > > > > 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 -- 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
