[gmx-users] Dummy atom in OPLS acetonitrile

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


Hi,

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.

Mark

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list