Hello,
I think you are mistaken. sander does NOT do normal mode analysis
calculations, nor does pmemd. The only options for calculating the nmode
entropy is to either use the nmode program itself or to use a nab program
that has an nmode call. You can use either MM/PBSA script as an example for
how to set up nmode calculations.
Good luck!
Jason
On Tue, Aug 3, 2010 at 5:50 AM, fancy2012 <fancy2012.yeah.net> wrote:
> Hi amber users,
> Is it possible to calculate entropy using normal mode analysis with pmemd?
> We know that it is sander usually, but pemmd is much faster. How could I do
> that? Thanks!
>
> All the best,
> fancy
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 03 2010 - 05:00:03 PDT
