question about rotation force in SMD

From: jnsong (
Date: Wed Apr 27 2011 - 09:34:09 CDT

Dear all,

Recently, I want to use SMD to research the mechanism about how a
membrane transporter transport its substrate through the lipid bilayer.

The transporter is a transport membrane protein and has six helix to
compact to be a cylinder in the lipid bilayer.

I suppose a mechanism that the transporter will rotate around the
bilayer normal at the same time the six helix change to an open state to
allow the substrate to travel through the channel.

So I have added a rotation force to allow the transporter to rotate
around an axis parallel to bilayer normal as told by the NAMD force

But the result is a little disappointing. The transporter just rotate
around the axis parallel to bilayer normal, but doesn't change to an
open state to allow the substrate to travel.

Would you someone please tell me what can I do to improve the result?

Should I increase the angular acceleration ongoing during the whole
simulation rather than keep it a constant value?
what is a reasonable value of angular acceleration?

The value of angular acceleration in my simulation is 1
My whole simulation time is 5ns.

Thank you very much!


Jianing Song
Ph. D. Student 
Institute of Theoretical and Computational Sciences
Dept. Phys.
East China Normal University
3663 North Zhongshan Road
Shanghai, P. R. China

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