VMD-L Mailing List
From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Fri Jan 25 2008 - 09:44:29 CST
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which reminds me to ask does NAMD support force DCD files?
(ok maybe this isn't a VMD question but namd used to have it namd v1.6
or so and if VMD users think it's worth having then NAMD might reenable
this option)
loading a coord DCD and a force DCD would provide a number of new
analysis options.
TOm
On Thu, 2008-01-24 at 18:01 -0600, John Stone wrote:
> Hi,
> You can load any scalar quantity you like into the per-atom-per-timestep
> "User" fields in VMD via scripts, and then use those values as the basis
> for coloring structural representations quite easily. Beyond that, you
> could go further and use some of the existing scripts people have written
> for drawing arrows and draw force arrows if that's something you're
> interested in. These sorts of things are all done via scripting as none
> of the standard simulation trajectory formats I'm aware of provide
> fields for storing these things. The main challenge here is just getting
> your force data into a file that you can then read into VMD using the
> scripts I mention above. Check out Axel's CPMD/VMD tutorial (linked to from
> the VMD tutorials page), as he's got some nice examples for
> drawing arrows and doing some of the items I've just described.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jan 24, 2008 at 06:16:14PM -0500, Yinglong Miao wrote:
> > Hi, VMD users/developers,
> >
> > Can anyone tell me whether VMD can visualize forces or not? I have some
> > force data calculated from a "pairInteraction" NAMD simulation and I'd like
> > to see how the forces on atom groups evolve as the simulation goes.
> >
> > Thanks in advance,
> > Long
> >
> > --
> > Yinglong Miao
> > Ph.D. Candidate
> > Center for Cell and Virus Theory
> > Chemistry Department, Indiana University
> > 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> > Tel: 1-812-856-0981
>
-- *********************** * Thomas C. Bishop * *Office: 504-862-3370 * *CCS: 504-862-8391 * *Fax: 504-862-8392 * ***********************
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