VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 06 2002 - 00:24:19 CDT

Will,
  Generally speaking its mostly an issue of getting a VRPN server
running for your Phantom. Getting VMD and NAMD up and connecting to
each other is actually quite easy once you've got a VRPN server on
the haptic device. In order to do IMD really well, you'll need a
minimum of 3 machines: one to run a VRPN server, one to run VMD,
and one (or several) to run NAMD. In our laboratory, we use PC's
running NT to drive the Phantom, and run the VRPN server. Most any
machine will do, we actually use a cheap laptop to run one of them,
so that particular Phantom can be carried to different rooms
(or to off-site demos) relatively easily. For VMD, you'll just need
a decent viz box, be it a workstation like a Sun/SGI, or a Linux box
with a GeForce board. For NAMD, you'll need the fastest box or boxes
you can get your hands on, we normally recommend using a PC cluster if
you've got one available locally. For best results something on the order
of 8 1GHz Athlons works quite well for many IMD simulations, though you
can use as many as 32 with good results, the performance has a lot to do
with the size of the simulated molecular system, and performance
characteristics of the cluster's network. You can of course run NAMD
on supercomputers or large shared memory machines if you happen to have
such machines available, they work well also.

The best way to start, if you haven't ever done this before, is to get
VRPN from UNC and get a VRPN server up and running. Once you've got that
going, then download and install VMD on one of your machines. From there,
you should be able to setup your .vmdsensors file specifying your local
VRPN server, and attach to it with VMD, even before trying a real simulation.
After that, you'll want to setup NAMD, and try connecting to a simulation.
One of the VMD developers (Paul Grayson) has written an easy-to-use script
for setting up and running IMD simulations, and this will make running the
simulations very easy once you've got each of the individual components
up and running.

Please let us know if you have any other questions. It may sound a bit
daunting at first, but its actually not too hard. Getting the Phantom
to cooperate with VRPN is often the biggest problem (since there are various
incompatible versions of the Phantom drivers and the Ghost toolkit...),
the rest of the process is typically quite smooth.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 06, 2002 at 01:11:34AM -0400, Will Sheffler wrote:
> VMD people,
>
> How difficult is it to get a PHANToM working with a VMD/NAMD
> interactive sim? Does anybody have practical experience doing this?
> We've got an PHANToM around somewhere and I'm thinking about playing
> with it...
>
> -Will Sheffler
> Graphics Group
> Brown University 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078