VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 18 2010 - 14:13:53 CDT

hi christian,

On Wed, Aug 18, 2010 at 12:04 PM, Christian Wohlschlager
<Christian.Wohlschlager_at_jku.at> wrote:
> Hello !
>
>
>  I set up a phantom desktop working via vrpn with  vmd, --> everything is
> working ok ( after patching vrpn code)
> maybe you have some cool examples with a force feed device,  i'm looking for
> a solution that i can touch the surface of a molekul to help a blind person
> having a idea of the geometry.

i have tried doing something like that
and found it to be very, very difficult to
get the right experience.

what you'd have to set up would be more
of a hard sphere model rather than a regular
force field calculation. you would have to use
a somewhat shorter time step and use a "probe
atom". that probe atom, would need to have a
very low mass, so that its momentum doesn't
interfere with the sensual experience. the interactions
with this probe atom would have to have a larger
than usual epsilon and would need their pair interaction
cutoff placed in the minimum of the potential, so
that it is only repulsive.

there is a "virtual AFM" input (for use with LAMMPS not NAMD,
though) at http://sites.google.com/site/akohlmey/software/vrpn-icms/
that is using some of those concepts. check out the
embedded youtube video and the explanations.

cheers,
     axel.

> thank you
>
>
> christian
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.