Nice idea! I will check it out. cheers!
On 6 January 2011 13:04, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> > > > _______________________________________________
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> > > > 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
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
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Received on Fri Jan 07 2011 - 03:00:02 PST
