VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 12 2003 - 14:27:54 CST

Dear Ioana,
  IMD simulations are a bit different from normal VMD operations.
VMD doesn't execute "force" commands when it communicates with the
running simulation. The current implementation allows you to store
the received simulation timesteps as they come in to VMD, but I've
forgotten if we have a Tcl queryable method for retrieving the forces
applied to the atoms over time. At present I'm thinking we don't,
but this is something that could probably be added if it is important
to you. In an old version of VMD we had code that wrote forces to a text
file, but that's long since been eliminated if I recall correctly.

If you just want to apply forces in a simulation, on different structures,
perhaps Tcl forces in NAMD are more what you need rather than recording
interactive forces in VMD? I'll CC this email to the NAMD team in case
they have any suggestions on this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 06, 2003 at 07:59:48PM -0800, Ioana Cozmuta wrote:
>
> Hi vmd users,
>
> I have a question related to the menu option
> Mouse/Force
>
> I am starting an NAMD simulation using IMD.
> I am applying a force with the mouse on a structure of which one end I
> fix.
> I am trying to write the commands into a logfile so that I can repeate
> that procedure to various structures however it seems that the Force
> command is not logged.
>
> Is there a reason for that? Is there a command that corresponds to this
> Force application?
> I would appreciate if I would get some more explanations on this.
>
> Thank you in advance,
> Ioana
>
> ****************************************************************************
> * Ioana Cozmuta, PhD * *
> * NASA-AMES Research Center * "Gravitation can not be held responsible*
> * Mail Stop 230-3 * for people falling in love" *
> * Moffet Field,CA 94035 * *
> * phone: (650) 604-0993 * Albert Einstein*
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-- 
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