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

[Paolo Costa]

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?*

Thanks.

Best regards,

Paolo

-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)