VMD-L Mailing List

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Mon Feb 07 2005 - 12:24:04 CST

If NAMD allows an SMD force to be applied on a selection of more than 1
atoms, then you can write a script to apply the same amount of force to
your selection of atoms. All these atoms will be subjected to the same
amount of external force in addition to whatever force they were
experiencing, and you should be able to move the COM "indirectly". Jim
may have better ideas.

Marc
On Feb 7, 2005, at 11:28 AM, Ekta Khurana wrote:

>
>
> Hello all,
> I want to do SMD by pulling the center of mass of two groups of
> atoms away from each other (two peptide rings). The way SMD is
> currently implemented in NAMD I can only pull one away from the
> other. Could someone suggest a solution for this? Can I use a TCL
> script for the purpose?
> Thanks in advance,
> Ekta
>
>