Dear Amber people, I was wondering if anyone of you can give me some
hints regarding the following issue.
I am currently using AMBER to simulate pure molecular and ionic
liquids, and I confront the simulation results (mainly radial
distribution functions, etc) with X-Ray diffraction data.
I would like to extend my analyses to spatial distribution functions
(i. e. of cations around anions, or polar groups in molecular
liquids), and I thought about using the grid command in ptraj to do
that. It read in the literature that it is normally been used to
visualize the distribution of water around solutes, e. g. proteins,
but in principle, I think that the method could be used also in my
case. Now the main point: in the SDF method (A. Vishnyakov, JPC A,
105, 2001, 1702), implemented, e. g. in mdynamix and gromacs tools,
the user needs to define the coordinate system for the calculation.
What happens with ptraj? Has anybody ever done a similar type of
calculation?
Thanks for any help
Regards
Lorenzo
--
=======================================
Lorenzo Gontrani
Research associate of EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
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Received on Wed Sep 21 2011 - 04:00:02 PDT
