Dear Justin, thanks for your extra description. Very nice! Last doubt, which values of "phase" and "pn" should I use for [ dihedraltypes ]?
Thanks again. Paolo Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul <jalem...@vt.edu> ha scritto: > > > On 4/26/20 2:08 PM, Paolo Costa wrote: > > Dear Justin, > > > > thanks a lot for your quick reply and useful information. > > Thus, I will go through to all the dihedral terms and define zero the > > corresponding force constant as you suggested. In any case, I guess it > will > > be too much work to calculate also the force constant for the torsion > angle > > rotation. > > Metals are usually the bridge point between multiple groups and as such > their dihedrals are all coupled and not generally considered "soft" > (rotatable). So the conformational energetics of these molecules usually > involves only bonds and angles in terms of internal parameters. > > -Justin > > > Thanks again. > > > > Paolo > > > > Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul <jalem...@vt.edu> > ha > > scritto: > > > >> > >> On 4/26/20 1:57 PM, Paolo Costa wrote: > >>> Dear Gromacs users, > >>> > >>> within Amber99 force field I created a new molecule, polyoxometallate, > by > >>> creating a new .rtp file and modifying the atomtypes.atp, > ffnonbonded.itp > >>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters > >>> from known works, while the parameters for the bonding interactions I > >>> determined by Gaussian together with VFFDT software. > >>> I did not insert any parameters for the dihedral angles since the > VFFTDT > >>> software does not calculated them. However as written in the related > >> paper > >>> (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation > >> related > >>> to metals can often be ignored".* > >>> Does somebody knows how to overcome such error in Gromacs? > >> pdb2gmx generates all possible angles and dihedrals, as determined by > >> the bonds that are defined in the .rtp entry. Thus, you likely have > >> dihedrals in the topology in which one of the participating atoms is the > >> metal. You have to have parameters for all defined interactions, but it > >> is true that dihedral terms are not typically used in this case. The > >> simplest solution is to define dihedrals with zero force constants so > >> they do not contribute to the forces in the system. > >> > >> -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. > > > > > > -- > ================================================== > > 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.
