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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Received on Thu Jan 06 2011 - 04:30:04 PST
