[gmx-users] Forcefield parameter for transition metal

[Srijan Chatterjee]

Hi Justin,
"The force fields in GROMACS are (by design) biomolecular in nature. None
support tungsten."
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
180-degree bond.
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?

Srijan


.......................................................................






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
> transition
> > metal.
>
> You'll have to start from scratch, likely. The force fields in GROMACS
> are (by design) biomolecular in nature. None support tungsten.
>
> -Justin
>
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-- 
SRIJAN CHATTERJEE