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
>
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