VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Nov 24 2003 - 18:24:47 CST

Hi,

I'll answer this one before I leave for another week...

VMD transmits raw forces to NAMD, rather than an actual potential
function. Therefore, there is no energy term due to the applied forces
(although you will certainly see an increase in the other energies due to
the work you are doing on the system). If you pull hard enough, you
should definitely see the atoms you are pulling on react.

At some point it would be preferable for VMD to send a potential function,
because this would allow NAMD's conjugate gradient minimizer to work
properly with a haptic device (currently you need to use the older
"velocityQuenching on" option if you want minimization in IMD).

Happy (American) Thanksgiving, be back Monday.

-Jim

On Tue, 25 Nov 2003, Harit Jani wrote:

> Dear Users,
>
> I am using PHANToM Haptic device for molecular simulation with VMD, NAMD, VRPN Server. I am doing IMD (Interactive Molecular Dynamics) for Alanin.
>
> My problem is what force (in unit say 30 Newton or something like that) would be applied by PHANToM on the molecule. I am getting some energy status output but on NAMD command prompt but how I can see the difference in energy status between “with PHANToM force feedback” and “without PHANToM force feedback” molecular simulation?
>
> Thank You,
>
> Harit Jani
> RMIT University, Melbourne
>
>
>