VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 21 2005 - 15:48:42 CDT

Hi,
  Is this script something that you want to run interactively,
i.e. calculate the applied forces based on user interaction, or
rather something that you want to be run in a more batch oriented mode.
If you going for a batch mode method of applying forces programmatically,
NAMD has its own Tcl forces interface for that purpose. If you want to
apply forced in a semi-interactive way via VMD, then you can use
the ufx, ufy, and ufz parameters to query and set user forces via
atom selections. e.g. $sel set ufx 4.0
The ufx/ufy/ufz parameters don't account for anything but the additional
IMD forces that VMD sends into the attached simulation. If you're doing
anything other than an IMD simulation, you'll want to use NAMD's own
Tcl forces interfaces for this sort of thing.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 20, 2005 at 11:38:18AM -0700, wmsmith wrote:
> Does anyone know if it is possible to write a TCL script that will assign
> forces to atoms/residues/etc. while the IMD is running. I know this can be
> done by using the mouse but I haven't seen any way to automate this using a
> script. 

-- 
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