From: luca belmonte (lucabelmonte_at_gmail.com)
Date: Wed Feb 04 2015 - 04:37:28 CST
I decided to go back to my parameters and check my QM calculations, from
the beginning, once more. They are pretty fine.
The second step was to "simplify" my molecular dynamic using just a
methanethiol group and a metal dication, using parameters I developed.
This latter attempt works pretty fine and respects the conformation that I
was expecting to have. Confirming that parameters are reliable.
Once more, the problem arose when I used the whole system I parameterized;
i.e. four methanethiol groups coordinating a metal dication.
A first solution, was to map everything in the "external bonds" and this
worked for me, even if some of the stuff need still to be fine tuned.
(When I say everything I mean the 4 bonds from S to M2+, 4 angles M2+ - S -
C, and finally 12 Dihedrals M2+ - S - C - H)
Now, I have two more questions:
1) I assume that this overwrite the parameters that I already mapped into
the par file, but, do you think it is a reliable approach? At the very
beginning I was planning to use this feature to map just the angles S-M2+-S
to keep the coordination sphere shape, but this does not work
2) When I remap, using external bonds feature, I need to use some dihedral
deltas of +- 120° in two out of the three M2+ - S - C - H, while one is
kept to 0°. Like for point 1, I'd like to have your opinion on this issue--001a11c368f8286332050e40c6c3--
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