How to put a COM restraint on a membrane protein?

From: A D (boltzmanndist_at_yahoo.com)
Date: Tue Oct 06 2009 - 18:03:25 CDT

Hi all,

In my simulation system I have a membrane protein embedded in a POPC bilayer. In 30ns, it unusually diffuses aggressively over several nm's in several directions whereas the experimental diffusion constant for a membrane protein is on the order of 10^-2 um^2/s. I could not really find the reason for this.

The main thing I am trying to do is to keep the protein in the center of the membrane. Therefore, I need to put a center of mass restraint on the protein but I could not find how to do this in NAMD. One possibility I thought was to use SMD commands with near zero velocity(absolute zero is not allowed). However, then you will be applying the SMD force in the direction of the vector "n" (SMDDir), because here is what you get when you differentiate the provided SMD energy function with respect to a coordinate vector of an atom: F=-k(vt-(R(t)-R(0)).n).n, which leads to a force vector in the direction of n. Therefore, I suppose using SMD is not the right thing. If anyone could suggest a solution to this, I will be grateful. Thanks a lot!!!

Seth

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