As an aside, you can always do this calculation by hand as well. Since the
surface tension variable is multiplied by every surface area, you can just
divide the average value of ESURF by the original surface tension and
multiply by your new one to get the new average value.
Since standard deviations don't involve such simple arithmetic as averages,
the same principle doesn't apply to standard deviations, but I don't expect
it would change much since you haven't changed the surface tension value
that much.
HTH,
Jason
On Tue, May 29, 2012 at 4:55 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> If you change parameters related to the actual energy calculations, then
> you will need to re-run the calculations. So if you want to change the
> cavity_surften variable, then you will need to re-run MMPBSA.py. The
> -rewrite-output command does not apply in this case.
>
> -Bill
>
> On Tue, May 29, 2012 at 5:59 AM, Cao Yang <muxiachuixue.163.com> wrote:
>
> > Hi everybody,
> >
> > I came across a problem in binding-free-energy calculation with MMPBSA.
> >
> > I calculated the binding-free-energy with the input file as below:
> >
> > Input file for running PB
> > &general
> > startframe=201, verbose=1,
> > /
> > &pb
> > istrng=0.100, cavity_surften = 0.03252
> > /
> >
> > Now I want to calculate the free energy again by changing
> "cavity_surften"
> > from 0.0378 to 0.0278. So I modify the input file and use the following
> > command:
> >
> > MMPBSA [original command-line arguments] -rewrite-output
> >
> > But the result of 0.0378 is just the same with 0.0278.
> >
> > Is it appropriate to use "-rewrite-output" here for time-saving purpose
> in
> > my case? Or should I redo the calculation when I modify "cavity_surften"
> > here?
> >
> > Many thanks!
> >
> > Cao Yang,
> > Zhejiang University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 29 2012 - 10:30:03 PDT
