[gmx-users] GAFF and alkynes

Justin Lemkul jalemkul at vt.edu
Thu Feb 12 13:47:15 CET 2015

On 2/12/15 4:40 AM, Rebeca García Fandiño wrote:
> 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?

The bond vibration issue is separate from angles being represented property. 
Likely you're not dealing with the linear angle properly (i.e. not defining it 
correctly in the topology).  Another approach is virtual site construction to 
define a linear moiety, as in my CO2 tutorial or as people have done for, e.g. 
acetonitrile (see the list archive).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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