[gmx-users] Forcefield parameter for transition metal
srijan9x at gmail.com
Thu Sep 5 09:14:28 CEST 2019
"The force fields in GROMACS are (by design) biomolecular in nature. None
Thanks for clarifying. I happen to just come across a paper with similar
forcefield values (https://doi.org/10.1016/j.jct.2019.01.016)
Although there is another problem with this molecule because of its
octahedral geometry. It contains several 180-degree bonds. So as from my
understanding of the CO2 tutorial gromacs has had difficulty in dealing
So, my question is
1) Do I have to use a virtual site to constrain the molecular geometry? If
so, for an octahedral geometry what should I do?
2) Is there any other way of doing it other than virtual site?
3)If I perform position restraint to each atom of 10000 still I can see
some movement of atoms but the molecule is not breaking. Is it bad or
reasonable approach to do it during MD?
On Tue, 3 Sep 2019 at 00:28, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 9/2/19 5:01 AM, Srijan Chatterjee wrote:
> > Hi,
> > I want to study tungsten hexacarbonyl in a solvent (acetonitrile).
> > I find that nither antechamber or PRODRG or OPLS automatic server
> support a
> > transition metal when creating input.
> > Can anyone guide me to create gromacs compatible parameter for a
> > metal.
> You'll have to start from scratch, likely. The force fields in GROMACS
> are (by design) biomolecular in nature. None support tungsten.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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