Re: SMD more than once

From: Eric H. Lee (
Date: Wed Aug 20 2008 - 14:39:37 CDT

Jarrod -

I'm not quite sure what you trying to simulate. Do you simply want to
simulate the system where the center of mass of the small molecule is
a fixed distance from the center of mass of your membrane? If so, why
not set the system up that way to begin with, and use heavy harmonic
restraints to hold them in place? If you want to say, pull your small
molecule through the membrane, then restraints on the membrane only
would be appropriate. More details would be needed to help me answer
your question.


On Aug 20, 2008, at 2:24 PM, JARROD EDWARD CHARLES NICKEL wrote:

> i would like to constrain the center of mass of a small molecule (20
> atoms) a set distance from the center of mass of a membrane (4256
> atoms). I tried using SMD with v=0 on the small molecule but my
> membrane began to drift away... Is there anyway i can use SMD on the
> small molecule and also use SMD on the membrane to hold both center
> of masses fixed? or maybe use harmonic constarints to hold one of
> the center of masses fixed, while just using SMD on the other?
> any help would be appreciated.
> Jarrod

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

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