Re: smd direction

From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Mon Mar 30 2009 - 12:59:29 CDT

Hi Ying,

You could also include components of the force to restore the position of
the pulled group along the actual line through which your atom should move,
using the SMD force as F = k(vt - Delta(x)), where Delta(x) should be the
actual displacement vector from the reference coordinates (composed by both
the parallel and perpendicular displacements, currently in NAMD the Delta(x)
is projected onto the pulling direction). Then, the force will have a
component perpendicular to the pulled line such that it will restore the
trajectory to that line. This is similar to applying constraints, but the
corresponding forces would appear in your SMD force modulus, thus being
quantifiable in the same pulling scene. This can be done with the TCL
scripting interface.

Leandro.

On Mon, Mar 30, 2009 at 1:39 PM, Eric H. Lee <ericlee_at_ks.uiuc.edu> wrote:

> 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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