smd dimer dissociation

From: L. Michel Espinoza-Fonseca (
Date: Tue Apr 25 2006 - 11:24:12 CDT

Dear all,

We're trying to setup a SMD simulation of the dissociation of a
monomer. I've been doing some research to see if somebody else has
done that before, and I found an interesting study on insulin. The
problem is that the authors use SMD to completely unfold the dimer.
What we're trying to do is to create some mutants on our protein and
then run SMD to see to what extent the mutations affect the stability
of the dimer. We do *not* want to unfold the dimer. So, here's my
question. Is there any way in which we can perform the SMD by pulling,
let's say, the center of mass of one monomer?

All suggestions are really welcome!!


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