[gmx-users] Dummy atom in OPLS acetonitrile

Mark Abraham mark.j.abraham at gmail.com
Mon Mar 13 21:00:47 CET 2017


It's problematic to implement a strictly linear molecule in any other way.
Various posts in the archives of this list touch on details, usually for
modelling nitriles or CO2.


On Mon, Mar 13, 2017 at 8:53 PM Thompson, Matthew White <
matt.thompson at vanderbilt.edu> wrote:

> According to virtualchemistry.org<http://virtualchemistry.org/>, OPLS
> uses a dummy atom ML in its acetonitrile molecule The oplsaa.ff/ files that
> ship with gromacs don't include a ML atomtype and the original
> parameterization (10.1002/jcc.1092) appears to also not include it.
> See http://virtualchemistry.org/molecule.php?filename=acetonitrile.zmat
> Does anybody know when this dummy atom was added? I know there are other
> compatible models out there but I am looking for discussion of why it was
> added.
> Matt
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