Dear Amber users,
I am trying to simulate an organic molecule containing an alkyne, using GROMACS and the GAFF force field.
The resulting structure from MD simulations is not correct, since the triple bonds should be linear (C-C=C-H), and I observe an angle among the atoms involved.
I have read in the past that GAFF did not reproduced very well the solvation energies of alkynes, but I had not seen anything related to the incorrect structure.
Thanks a lot for you help in advance!
Rebeca
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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Received on Thu Feb 12 2015 - 02:00:02 PST
