Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus keeping constant the distances between the different metal and oxygen atom".* That means they did not parametrize the bonded interactions for such molecule, isn't?
Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:20 Justin Lemkul <jalem...@vt.edu> ha scritto: > > > 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 > > -- > ================================================== > > 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 > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.