On Thu, Feb 12, 2015, Rebeca García Fandiño wrote:
> 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.
What is the angle you see? What angle do you get if you minimize the
structure? Linear molecules can be difficult for molecular mechanics force
fields, since the angle force becomes poorly defined near 180 degrees.
...dac
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Received on Thu Feb 12 2015 - 04:30:03 PST
