Hi,
Unless you are using an old version of cpptraj, the Gist output contains
three entropy columns: dTStrans, dTSorient, and dTSsix (all in _dens and
_norm variants). dTSsix is the entropy estimated from the combined space
of translations and rotations, and is approximately equal to dTSorient +
dTStrans. Generally, it is advisable to use dTSsix if the split into
translational and orientation contributions is not needed.
There have been studies that also evaluate parts of the second order
entropy, but this requires much more sampling of the water conformations
and has not been implemented in cpptraj.
The study you cite (
https://doi.org/10.1021/acs.jctc.5b00939), evaluates
the second-order translational entropy on a grid. There is also a
publication by our group (
https://doi.org/10.1007/s10822-021-00429-y),
in which we approximate this problem by a 1D rdf computed at every grid
point. While this certainly means that we lose some information, it
simplifies the convergence of the results.
Best regards,
Franz
Am 08.03.2022 um 14:44 schrieb Daniella Hares:
> 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 Thu Mar 24 2022 - 10:30:02 PDT
