Re: Calculation of PMF between protein domains NAMD

From: Chola Regmi (
Date: Wed May 13 2015 - 18:14:49 CDT

Hi all,
I found that there is a small helix in the middle of long loop at the
interface of two domains. I used metadynamics and found that extension of
loop takes place rather than dissociation of domains while it samples the
distance. I used COM distance between two domains as a reaction coordinate.
Also I tried SMD pulling through COM of that domain with additional
movingConstraint on the helix part which is equal to SMD velocity (1A/ns).
In this case I am able to dissociate the domains with reasonable force
graph but in physically how can I justify the role of movingconstrain on
helix part and PMF result ? I will highly appreciate your suggestions.


On Fri, Apr 17, 2015 at 7:50 PM, Chola Regmi <> wrote:

> Thank you all for your valuable suggestions. I would go through the above
> mention paper first and will choose proper sampling method as you mention--001a11407776133bdb0515fec77a--

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