Dear all AMBER users,
I have a query regarding how the entropy is calculated in CPPTRAJ implementation of GIST.
According to the paper below, the first-order entropy is evaluated using two different methods, but the GIST output has only two entropy quantities - the first order translational and orientational entropy densities - implying one method is used. Does anyone know which method is used in practice?
S. Ramsey, C. Nguyen, R. Salomon-Ferrer, R. C. Walker, M. K. Gilson and T. Kurtzman, J. Comput. Chem., 2016, 37, 2029-2037. (doi: 10.1002/jcc.24417)
Additionally, the Amber21 manual states that the higher-order entropies are not yet computationally accessible, but there have been papers with extensions to GIST that account for this - for example, below. Are any corrections used in the CPPTRAJ implementation of GIST?
C. N. Nguyen, T. Kurtzman and M. K. Gilson, J. Chem. Theory Comput., 2016, 12, 414-429. (doi: 10.1021/acs.jctc.5b00939)
Any help would be appreciated.
Best wishes,
Dani Hares
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
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Received on Tue Mar 08 2022 - 06:00:02 PST
