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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 29 2012 - 05:00:03 PDT
