VMD-L Mailing List

From: George Patargias (gpat_at_bioacademy.gr)
Date: Tue Oct 30 2012 - 05:57:26 CDT

Many thanks for your reply; it really clarified a lot.

Just a couple of more things, if you don't mind, that occurred to me as I
went through the set-up requirements listed in your page.

One requirement is the libnifalcon library. Does the installation of
libnifalcon come before or a after VRPN installation? How the two
installations relate?

In .vmdsensors file, am I right to understand that in
"vrpntracker://localhost/Tracker0"

"localhost" is the IP address (or hostname?) of the machine that Falcon is
connected?

Do you have any idea which type of USB-2.0 hub would be suitable for a
MacOS laptop? In the instructions for calibrating the device and loading
the firmware you say that the firmware (after second/third attempt) will
not load if the USB is not suitable.

Is there any standard way to choose TCP port numbers for the VMD/IMD and
VRPN/VMD connections?

Thanks again.
George

> On Fri, Oct 26, 2012 at 1:01 PM, George Patargias <gpat_at_bioacademy.gr>
wrote:
>> Hello
>> Apologies if this is too trivial. I am trying to figure out how to
connect/use the Novint Falcon device for IMD with VMD/NAMD.
>> As far as I understand, the VRPN-ICMS software (from Dr Kohlmeyer's
page)
>> provides an interface between Falcon and VMD; is this correct? If so it
> yes. the regular VRPN distribution should work as well,
> since the code has been folded into VRPN quite a while back.
>> needs to to be installed in the the machine where the IMD will run?
> no. please keep in mind that you have two connections (and
> both use TCP/IP sockets). the IMD connection between the
> ongoing simulation and VMD over which VMD receives updated
> coordinate information and tells the simulation about adding
> forces to atoms that are communicated via IMD.
> and then you have the connection from VMD to the haptic device
> via VRPN which tells VMD the position of the effector or "3d mouse"
(which is used to compute the forces to be send to the simulation via the
IMD connection) and through which VMD tells VRPN what
> force feedback to generate on the haptic device.
> i know about a 4-way setup that was run at a supecomputing
> conference:
> 1: supercomputer to run the MD simulation on
> 2: remote visualization facility to run VMD on
> 3: laptop machine to run VRPN on
> 4: multiple desktops to run the viewer for the remote viz on.
> it is also possible to connect multiple haptic devices
> via separate VPRN instances, eg. on multiple laptops
> and then have a tug-o-war between them. theoretically,
> the falcon support in VRPN would handle multiple falcons
> from the same instance, but there are some nasty issues
> with initializing the device, that can be avoided by using
> a separate host for each falcon.
>> I am asking because I have seen pictures in which haptic devices are
connected/controlled by a separate machine (e.g. a laptop).
> yes. that is how it works. with the way how the IMD
> support is implemented in LAMMPS, you can also
> easily have multiple IMD connections to the same simulation.
>> Apart from VMD, NAMD and VRPN-ICMS no other additional package is
needed
>> to run an IMD?
> you don't necessarily need NAMD as MD code. several other MD codes
(LAMMPS, HOOMD, Gromacs) also support the IMD protocol.
> hope that helps,
> axel.
>> Thanks in advance.
>> George
>> Dr. George Patargias
>> Postdoctoral Researcher
>> Biomedical Research Foundation
>> Academy of Athens
>> 4, Soranou Ephessiou
>> 115 27
>> Athens
>> Greece
>> Office: +302106597568
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.

Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568