Thanks Justin. I will then add manually the constraints on the topology file.
Paolo Il giorno gio 7 mag 2020 alle ore 14:56 Justin Lemkul <jalem...@vt.edu> ha scritto: > > > On 5/7/20 8:53 AM, Paolo Costa wrote: > > Dear Justin > > > > that means when I generate the topology file by pdb2gmx I will add > manually > > the section [constraints] on it? > > I suggest you look into the manual to understand different ways of > applying constraints. You can either convert bonds into constraints via > the "constraints" .mdp option, in which case the force constants are > irrelevant but the equilibrium lengths matter, or you do not define any > bonds and manually write in the [constraints]. It depends on how you > need to treat the system. I know nothing about POMs so I can't comment > specifically. If the species is treated as a fully rigid entity (not > something GROMACS is really well suited for), then you should probably > be writing the topology manually because you will have lots of bonds to > non-sequential atoms. > > -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.