On 5/6/20 11:35 AM, Paolo Costa wrote:
Dear Gromacs users,

I am interested on studying the interaction between large metal cluster
anions (polyoxometallates, POM) with different organic cations (e.g
perylenes, etc..) in water.
I have already the non bonded parameters of POMs from literature, while the
bonded parameters I calculated from Gaussian and VFFDT software.
If I do not apply a position restraining force on the POM atoms, the POM
structure gets distorted too much from the experimental one. I guess this
is due to the lack of a good force field parametrization for
metal-containing compound.
*Thus, my question is the following:*
*can I keep applying a position restraining force on POM atoms during the
minimization, equilibration and production steps or is it conceptually
wrong?*

If you're restraining a configuration because the force field is so bad, I'd immediately be skeptical of the quality of any simulation. Bonded parameters are generally easy to reproduce and probably aren't the source of your problem if you've implemented them carefully, but if you're trying to combine new bonded parameters with existing nonbonded parameters, you need to do careful validation on a known system.

If your system doesn't work, you should back up and make sure you can reproduce a published study using the same parameters and not ones of your creation.

-Justin

--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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