Re: SMD force (fwd)

From: Ioana Cozmuta (
Date: Tue Jan 06 2004 - 18:25:20 CST


Thank you for your reply.

On Tue, 6 Jan 2004, Fangqiang Zhu wrote:

> > It is not clear to me what exactly does "current force applied to the
> > center of mass" means:
> > a. force due to dragging of the atoms with velocity v via a harmonical
> > constraint k
> > b. force due to the interaction with the surroundings
> > c. both dragging force and interaction with the surroundings
> The answer is a.
> > I want to use the information in the output to calculate only the
> > component due to the interaction between the restrained atoms and the
> > surroundings.
> Currently the only way to get the force on an atom arising from other
> atoms (in your word, the surroundings) in the simulation is to use the Tcl
> command "loadtotalforces". Please read the manual carefully for its
> usage.

I have the information in SMD
SMD time position (r_cm) force (F_drag)
This means that I can calculate the interaction force two ways:

1. from Newton's EOM:
F_interaction = m*a-F_drag (where a can be approximated from every three
values of the r_cm in the SMD output)

2. From the pairInteraction module in NAMD as sum of vdw and electrostatic
F_interaction = F_vdw+F_electrostatic

So in principle no matter if I use 1 or 2 I should get aprox the same
value. Did anyone get to check this equality?


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