Dr. Steinbrecher
Thanks a lot for your detailed explanation. It certainly helps to clarify
some of my understanding of the TI calculations. Appreciate it.
Victor
On Sat, Dec 10, 2011 at 5:14 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi Victor
>
> > This is my mdin_min_v0_l05 file:
> > ................
> > ifsc=1, crgmask='',scmask=':REF.A1',
> > .................
> > ifsc=1, crgmask='',scmask=':NEW.B1,B2',
>
> yes, that is what I meant. Be careful though, now all atoms except A1, B1,
> B2 need to have identical starting positions in both processes and they
> must occur in the same order in the molecule.
>
> > And if i'd like to do the 2-step as a comparison, I should try this:
> > step1: (here use ref.prm for v1 and new.prm for v0)
>
> your step two looks ok, but there need to be two separate charging steps.
> Check out the table at:
>
> http://ambermd.org/tutorials/advanced/tutorial9/setup.html
>
> for an example of this type. Only one of the runs would use softcore
> potentials, the first and third are linear coupled between two different
> charge states only.
>
> > I hope I get the direction right. Correct me if I'm wrong. Thanks a lot.
>
> The directions of each step dont matter, as long as you sum up the deltaGs
> correctly. The important thing is that the sum of all steps needs to be
> exactly your overall transformation, e.g. all changes in potential
> function are explicitly considered.
>
> Kind Regards,
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Sun Dec 11 2011 - 09:30:03 PST
