Re: smd direction

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Mon Mar 30 2009 - 11:39:17 CDT

The force *is* being applied in that direction (-1,0,0). However,
since you are compressing your protein, there are other forces at play
here. Those forces, combined with your SMD force, may perturb the
position of your SMD atom along the vector you specify. You may wish
to apply harmonic constraints along the Y and Z axes to restrict the
position of your SMD atom along the X-axis - however this constraint
will limit the degrees of freedom your polymer can sample and produce
a compression which records artificially high forces beyond those
produced by the SMD force.

-Eric

On Mar 30, 2009, at 11:15 AM, Wang,Ying wrote:

> 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!
>
>
> Best,
>
>
>
>
> On Mon Mar 30 11:52:05 EDT 2009, "Eric H. Lee" <ericlee_at_ks.uiuc.edu>
> 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
>> ericlee_at_ks.uiuc.edu
>
>
>
> --
> Wang,Ying

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

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