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.
