Dear Jason,
Thanks very much for your detailed explanations! I have just understood that! Thanks!
All the best,
fancy
>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 - 05:00:05 PDT
