Determining Equillibration of a membrane protein

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Tue Jun 26 2007 - 18:57:32 CDT

Hello All,

Can anyone comment on an optimal way to determine if a protein has
equillibrated. I am currently running a large membrane protein simulation (
i.e. membrane/protein/water). As expected the energy and volume of the
simulation equillibrated in about 400 ps.

So I am determining equillibration based on the RMSD of the protein relative
to the crystal structure. My only concern is that the RMSD is still going
up an may never level off. Any thoughts?

Thanks,

Ilya Chorny Ph.D.

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