You cannot do a quasi harmonic approximation with just one frame. It is
very important that you try to understand the theory behind the method
before using it. Otherwise, you can never truly understand or trust the
results.
Adrian
On 9/3/13 10:06 PM, Xioling Chuang wrote:
> Dear Jason,
> Thank you very much again for your message.
> I have tried to calculate entropy using quasi-harmonic approximation with MMPBSA.py. The input is
>
> &general
> startframe=1, endframe=1,
> interval=1, keep_files=0,
> verbose=1,
> entropy=1,
> /
> &gb
> igb=2, saltcon=0.0,
> /
>
> I got three lines of warning message as
> "Warning in analyzeMatrix: bad eigenvalue 0 0.00"
> and the entropy result is 0.00 for all Tran., Rot. and Vib.
>
> Please suggest.
>
> Best Regards,
> Xioling
>
>> I don't know. They use their own set of programs/scripts to handle it. I
>> would suggest reading their papers and/or visiting their website for hints.
>> This is not implemented directly by any Amber programs, so it may be that
>> nobody that responds on this list knows.
>>
>> Good luck,
>> Jason
>
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--
Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Sep 03 2013 - 19:30:02 PDT
