Re: What decides the pulling direction in SMD?

From: David Tanner (
Date: Fri Jun 12 2009 - 07:04:27 CDT

The NAMD user's guide page on SMD:

explains how the user
chooses the the vector along which the atoms are moved, and that the
atoms are only constrained to move along this vector by a harmonic
constraint; so they are allowed to deviate somewhat from the
designated path if the spring constant is sufficiently small.

Thank you,
David E. Tanner

David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801

2009/6/12 李璀 <>

> Dear all,
> I am doing my SMD with a protein-ligand complex, while the protein has
> 2 ports for the ligand to escape. I firstly chose a velocity, about
> 0.5A/ps and a direction that the ligand could leave from the protein via
> port1 quickly, and the program did so. However, when I kept the direction
> but changed the velocity to a smaller one, about 0.03A/ps, the ligand got
> out from the other port--port2. And when the velocity changed to 0.01A/ps,
> the ligand came back to leave from port1 . I cant't understand what decides
> the direction of the pulling direction in SMD. Would anyone tell me? Thanks
> a lot.
> Tracy Lee
> ------------------------------
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