[gmx-users] Forcefield parameter for transition metal
jalemkul at vt.edu
Fri Sep 6 16:13:33 CEST 2019
On 9/5/19 3:07 AM, Srijan Chatterjee wrote:
> 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?
Try using the 180-degree angle. I wrote the virtual site tutorial when
GROMACS could not handle such a case but I believe the code changed some
> 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?
10000 is a rather strong force constant, but as with any restraint, it
will never prevent motion, only disfavor it.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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