If I'm understanding what you're looking for, then this is something you'll
have to "fake" with a visualization program. At the end of the day, an atom
is either *there* or it's *not* as far as VMD or Chimera is concerned. You
can create a new representation for the part that you are morphing in TI and
generate new materials with different levels of transparency, making one
fade in while another fades out as you change lambda.
Hope this helps,
Jason
On Thu, Jan 6, 2011 at 7:04 AM, g t <sketchfoot.gmail.com> wrote:
> Hi, I think I see what you mean. I think my error was in thinking that a
> single topology was being used and could thus be viewed visually. Thanks
> for
> your quick answer.
>
> Best regards,
> GT
>
> On 6 January 2011 10:36, <steinbrt.rci.rutgers.edu> wrote:
>
> > Hi,
> >
> > I'm not perfectly sure what you mean, but my guess is the answer is no.
> > Due to the dual topology model, Amber will propagate both sets of atomic
> > coordinates in parallel, there is no such thing as 20% of a coordinate.
> So
> > your end state prmtop files will work on the crd-files at any lambda from
> > zero to one.
> >
> > You can visualize your trajectories in VMD of course, you will see atoms
> > behaving as if they only feel e.g. 20% of the interaction strength they
> > had at the initial state.
> >
> > Kind Regards,
> >
> > Thomas
> >
> > On Thu, January 6, 2011 2:02 am, g t wrote:
> > > Hi,
> > >
> > > Is there any way to get amber to write a parm file that represents the
> > > structure used for lambda points between 0 and 1, (e.g. 0.., 0.2, etc)?
> > > That
> > > way, the trajectory could be visualised in a viewer such as chimera or
> > > VMD.
> > > The reason I am enquiring about this is that I am interested in
> preparing
> > > a
> > > series of graphics that explain the lambda concept to people unfamiliar
> > to
> > > it in presentations, etc.
> > >
> > >
> > > Cheers!
> > > GT
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > Dr. Thomas Steinbrecher
> > formerly at the
> > BioMaps Institute
> > Rutgers University
> > 610 Taylor Rd.
> > Piscataway, NJ 08854
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 06 2011 - 05:30:02 PST
