[AMBER] Polarizability and induced dipoles

From: Mag. Thomas Taylor <thomas.taylor.univie.ac.at>
Date: Tue, 15 Jun 2010 10:53:33 +0200

Dear AMBER users and developers,

Please find attached two patches:
- chamber.patch
- dipoles.patch

chamber.patch:
The created prmtop file now always has a POLARIZABILITY flag. Either it contains
only 0s or the polarizability data extracted from the prm file.

dipoles.patch:
To calculate properties from the trajectory I require the induced dipoles for
each atom. According to the documentation one can define groups and then output
them to the out file or something, but I feel it should be possible to store
them in the trajectory file along with coordinates and velocities.
For this purpose I have cannibalized the -mdip command line options as it
appeared to be unused.
Also introduced is the parameter ntwm in the namespace control, which behaves
for dipole archiving (storing) like ntwv does for velocities.

Please consider incorporating parts or all of the patches into AMBER11.
Feel free to point out any bugs/problems/etc.

HTH,
Thomas Taylor


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Received on Tue Jun 15 2010 - 02:00:03 PDT
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