From: David Tanner (dtanner_at_ks.uiuc.edu)
Date: Fri Jun 12 2009 - 07:04:27 CDT
The NAMD user's guide page on SMD:
http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node41.html
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
http://www.linkedin.com/in/davidetanner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2009/6/12 李璀 <letitgone_at_hotmail.com>
> 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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