Re: smd direction

From: Wang,Ying (
Date: Mon Mar 30 2009 - 11:15:06 CDT

Thanks a lot for your explain! But in this simulation, I use
constant velocity but not constant force SMD. I guess that the SMD
atom should move along the direction I gave.

If you have any idea how to let the SMD atom move as I wish could
you tell me? Thank you very much!


On Mon Mar 30 11:52:05 EDT 2009, "Eric H. Lee"
<> wrote:

> 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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