[gmx-users] GAFF and alkynes

Rebeca García Fandiño regafan at hotmail.com
Thu Feb 12 10:40:24 CET 2015

Dear Gromacs users,
I am trying to simulate an organic molecule containing an alkyne, using GROMACS and the GAFF force field. 
When I do grompp I get this note, referring to the atoms involved in the triple bond:

NOTE 1 [file ligando_gmx.top, line 289]:
  The bond in molecule-type solute between atoms 17 C12 and 18 C8 has an
  estimated oscillational period of 1.7e-02 ps, which is less than 10 times
  the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

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.

Maybe GAFF is not well optimized for alkynes, or maybe the NOTE suggested by GROMACS is the responsible for this incorrect structure?

Thanks a lot for you help in advance!


Dr. Rebeca Garcia
Santiago de Compostela University


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