Re: smd direction

From: Eric H. Lee (
Date: Mon Mar 30 2009 - 10:52:05 CDT

While the direction the force is being applied is indeed (-1,0,0), you
did state that you were compressing a polymer, and as such, steric
clashing may produce forces which push the molecule in a different
direction than the SMD force is being applied. During the simulation,
the force is being applied along the correct vector though.

- Eric

On Mar 30, 2009, at 10:04 AM, Wang,Ying wrote:

> Hi, dear all,
> I have a question about the SMD direction.
> In my case, I let the polymer align along the x axis. Then I fix one
> end and push the other end toward (-1,0,0) direction, which is like
> a "compression" process.
> However, during the process, the SMD atom didnot move as I set. It
> moves along (-0.8,-0.4,-0.5) roughly. But in the log file, the SMD
> direction is (-1,0,0) indeed.
> Could anybody tell me what's happen? If I compress the polymer, the
> SMD atom will adjust the direction by itself if the force too large?
> How can I let it move as I wish?
> Thanks a lot!
> --
> Wang,Ying

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

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