VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 16 2014 - 15:36:15 CDT

Hi,
  Force values are not reported except if you setup a
per-frame update callback that prints out the values for yourself.
You can query them from an atom selection with:
  $sel get {ufx ufy ufz}

The forces don't really have directly meaningful units as VMD doesn't know
what the coordinates or other units on the other end of the IMD connection
necessarily are, and the simulation program on the other end is free to
interpret the forces in whatever way it wants. So, the meaning of the
force values is specific to the simulation code you're linked to,
and any runtime options or scaling parameters that are being applied to
the forces as part of the simulation code.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 16, 2014 at 12:06:22PM +0300, George Patargias wrote:
> Hello,
> I know that forces can be applied in VMD (during an IMD) using the Mouse
> menu of the VMD Main window and then select "Mouse -> Force -> Fragment"
>
> Where the the value of the applied force is reported?
>
> Thanks.
>
>
> > George,
> > Yes, we'll have to get you a new VMD so that it will see VRPN,
> > but we can help you with that once you get VRPN talking to the Falcon.
> > Which VRPN version are you using by the way?
> >
> > Cheers,
> > John
> >
> > On Wed, Oct 15, 2014 at 06:34:41PM +0300, George Patargias wrote:
> >> Hello
> >>
> >> Thanks for your reply. The issue is that VRPN can't see the Falcon -
> >> sorry
> >> for not being clear. Maybe it needs a powered hub to work as Axel has
> >> pointed out.
> >>
> >> As far as I can tell, VMD 1.9.1 that I am currently running can see
> >> VPRN
> >> because when I try to create a "tug" type of tool I get the message in
> >> VMD terminal
> >>
> >> VRPN Error
> >> from Tracker0: No response from server for >= 10 seconds
> >>
> >> Best
> >> George
> >>
> >> > Hi,
> >> > VMD can't directly talk to the Falcon, instead, it communicates
> >> > with VRPN, and VRPN takes care of directly communicating with the
> >> > Falcon. From your note it wasn't entirely clear if the issue is
> >> > that VRPN can't see the Falcon, or if VMD can't see VRPN. If the
> >> > problem is that VRPN can't see the Falcon, then I will have to defer
> >> > to the expertise of others here that have used the VRPN servers with
> >> > the Falcon and see what suggestions they have.
> >> >
> >> > If the problem is that VMD can't talk to VRPN, then the most likely
> >> issue
> >> > is that we need to get you a VMD binary that is compiled against a
> >> newer
> >> > version of VRPN, because previous VMD binaries were compiled against
> >> an
> >> > old VRPN version that is now out of date. If this is the problem, I
> >> can
> >> > help you get this done, as it is on my TODO list for the new VMD 1.9.2
> >> > release, and it would be great to have people test it out.
> >> >
> >> > Cheers,
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> >
> >> > On Wed, Oct 15, 2014 at 06:07:29PM +0300, George Patargias wrote:
> >> >> Hello,
> >> >>
> >> >> I was wondering whether VMD can be configured to communicate with the
> >> >> Novint Falcon haptic if the latter is controlled with the Windows
> >> >> drivers
> >> >> provided by Novint.
> >> >>
> >> >> I have compiled and installed VRPN on my Linux desktop but for some
> >> >> reason
> >> >> the VRPN server doesn't recognize it.
> >> >>
> >> >> Thanks.
> >> >>
> >> >> George
> >> >>
> >> >>
> >> >> Dr. George Patargias
> >> >> Postdoctoral Research Fellow
> >> >> Biomedical Research Foundation
> >> >> Academy of Athens
> >> >> 4, Soranou Ephessiou
> >> >> 115 27
> >> >> Athens
> >> >> Greece
> >> >>
> >> >> Office: +302106597568
> >> >
> >> > --
> >> > NIH Center for Macromolecular Modeling and Bioinformatics
> >> > Beckman Institute for Advanced Science and Technology
> >> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >> > http://www.ks.uiuc.edu/Research/vmd/
> >> >
> >>
> >>
> >> Dr. George Patargias
> >> Postdoctoral Research Fellow
> >> Biomedical Research Foundation
> >> Academy of Athens
> >> 4, Soranou Ephessiou
> >> 115 27
> >> Athens
> >> Greece
> >>
> >> Office: +302106597568
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
> >
> >
>
>
> Dr. George Patargias
> Postdoctoral Research Fellow
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568 

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