Re: How are the SMD atoms connected to the center of mass

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Dec 02 2009 - 07:45:26 CST

In another topic

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/10649.html

David provided the following explanation:

"The center-of-mass doesn't put a velocity on the atoms, it puts a force on
the other atoms. Each atom being pushed is connected to the center-of-mass
by a spring. Each atom then gets dragged along by those springs."

So does anybody know how the magnitude of this springs are selected? Isn't
it important since it has an effect on the conformation of the structure
attained during pulling?
Best,
Mert

On Tue, Dec 1, 2009 at 3:31 PM, Mert Gür <gurmert_at_gmail.com> wrote:

> Dear all,
> I got one more question today,
> For SMD it is indicated that "The center of mass of the SMD atoms will be
> harmonically constrained with force constant k (SMDk) to move with
> velocity v".
> If I select multiple atoms to be the SMD atoms how are they connected the
> center of mass that is pulled? Are their position fixed with respect to the
> center of mass or are they connected with an spring to the COM.
> Best,
> Mert
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:34 CST