[gmx-users] Info regarding restrained minimization, equilibration & production

Justin Lemkul jalemkul at vt.edu
Thu May 7 14:20:24 CEST 2020

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 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

jalemkul at vt.edu | (540) 231-3129


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