# Re: SMD on center of mass

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Nov 02 2006 - 21:27:41 CST

I have found part of the answer myself by looking into the code
(GlobalMasterSMD.C):

GlobalMasterSMD::GlobalMasterSMD(BigReal spring_constant, BigReal
velocity,
const Vector direction, int output_frequency,
int first_timestep, const char *filename) {

...

BigReal diff = (curcm - cm)*moveDir;
Force f = k*(moveVel*currentTime - diff)*moveDir;
modifyGroupForces()[0] = f;

The force "f" is calculated based on the displacement of the center of
mass. However, from the line "modifyGroupForces()[0] = f;" it seems that
the calculated force is applied to each SMD targeted atom. Does this mean
that the more targeted atoms I have the higher will be the force applied
to the whole group of SMD atoms? Conversely, in the documentation for TMD
I read that the spring constant "k" is scaled down by the number N of
targeted atoms. This does not seem the case for SMD. Am I right? What does
the line "modifyGroupForces()[0] = f;" exactly do? Does it apply "f" to
each atom or is the force split equally among the targeted atoms? In the
first case, does it make sense to set SMDk = k/N, where "k" is my
"intended" spring constant and "N" the number of targeted atoms?

I would appreciate any help to get this clear.

Gianluca

On Thu, 2 Nov 2006, Gianluca Interlandi wrote:

> I'm sorry. This is the second e-mail I'm posting about this issue. Again a
> question about what I read in the documentation:
>
> > The center of mass of the SMD atoms will be harmonically constrained with
> > force constant"k" (SMDk) to move with velocity "v" (SMDVel) in the
> > direction "n" (SMDDir).
>
> SMD thus results in the following potential being applied to the system:
>
> U(r_1, r_2, ..., t) = 1/2 k [vt - (R(t) - R_0) . n ]^2.
>
> What is the SYSTEM? Is it the whole protein or just the SMD atoms?
>
> Thanks a lot,
>
> Gianluca
>
> -----------------------------------------------------
> Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://biocroma.unizh.ch/gianluca/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4435
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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