[gmx-users] Re: Com Pulling

[lloyd riggs]

Dear All,

I was setting up things to use COM pulling for a multiprotein complex.  My question after going through the gromacs documentation(online) is:

Is there a way to limit either the time or distance two groups are pulled towards each other(reguarding only the applied force), as I could not find anything.  Basically, if I run something in vacuo, the groups (proteins) do not move globally even when constraints, etc are set to none.  To measure any Gibbs , delta H etc...I need the groups too move towards each other and form the interactions I am measuring, but do not want the pull force to interfear with overall calculations.

My thoughts were to do a very short run, and then either remove the pull force, etc from the .mdp file, and use a checkpoint to re-start it, but do not know if this would work or would maintain the movement however arbitrary in the general correct direction.

that or use such a small (.2 kcal/mol nm2) that it does not matter very much.

Sincerely,

Stephan Watkins
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