VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 12 2003 - 17:18:12 CST

Ioana,
  I consulted with Justin on this and in fact you can get the IMD
forces by doing an atom selection and querying for 'ufx', 'ufy',
and 'ufz'. With that, looping over all of the saved IMD
simulation frames, you could write out a force file. From there,
one could write a NAMD Tcl script to apply the forces in subsequent
simulations. NAMD is flexible enough to allow you to change the
applied forces over time, it can do much more than just a fixed
force. I'll CC the NAMD team in case they have any comments on
where the Tcl forces features are documented and what limitations
they may or may not have as it applies to your problem.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 12, 2003 at 12:36:26PM -0800, Ioana Cozmuta wrote:
> Hi John,
>
> Thanks a lot for your reply. I think the equivalent in NAMD would be to
> apply a constant force. The difference is that with IMD you can apply the
> force in the direction you want and then also remove it when you think it
> has done its job. In NAMD the constant force that you apply is there for
> the duration of the simulation so the only way I could come up with was to
> design a file where I apply 5ps a force then remove it then apply it again
> in another direction. I was just wondering if there was a more simple way
> and also a reproducible way using IMD.
>
> I would appreciate any suggestions.
>
> Thank you,
> 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*
> * fax: (650) 604-0350 * (1879-1955) *
> ****************************************************************************
>
> On Wed, 12 Mar 2003, John Stone wrote:
>
> >
> > 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*
> > > * fax: (650) 604-0350 * (1879-1955) *
> > > ****************************************************************************
> >
> > --
> > 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
> > 

-- 
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