Re: smd dimer dissociation

From: Leandro Martínez (
Date: Tue Apr 25 2006 - 12:10:13 CDT

Sure there is. Yo only need to set the "SMD atoms" in the
SMDFile of namd as all the atoms of one of the monomers. Then
the center of mass of the atoms will be pulled. Whether or not
your monomer will unfold is probably related to the pulling velocity.

On 4/25/06, L. Michel Espinoza-Fonseca <> wrote:
> 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!!
> Thanks!
> Michel

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