[gmx-users] Re: Pulling ion - US

Steven Neumann s.neumann08 at gmail.com
Wed Dec 12 14:41:43 CET 2012

Thank you all!

On Tue, Dec 11, 2012 at 12:54 PM, Leandro Bortot <leandro.obt at 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.


> 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
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