Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it?
Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:50 Justin Lemkul <jalem...@vt.edu> ha scritto: > > > On 5/7/20 8:47 AM, Paolo Costa wrote: > > Dear Justin, > > > > I thought too. > > In case, could you please indicate me how I can constrain the interatomic > > distance of a desired molecule, in such case the POM molecule? > > Define [constraints] in the topology for all relevant interatomic > distances. > > -Justin > > > Thanks a lot. > > > > Paolo > > > > Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul <jalem...@vt.edu> > ha > > scritto: > > > >> > >> On 5/7/20 8:41 AM, Paolo Costa wrote: > >>> 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? > >> That sounds to me like all interatomic distances were fixed via > >> constraints, but you should contact the corresponding author to be sure, > >> and ask for example inputs. > >> > >> -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.
