Dear GMX community, I am running simulations of a solvated protein on a (frozen) Au substrate, but I think that my question is so basic that it falls outside the details of my case...
So, the question is: when I prepare the system by minimizing the energy, should I set constraints = all_bonds, h_bonds or none? IMHP, I should set it to all_bonds, otherwise I may risk that the system's energy minimum corresponds to a configuration very different from the initial one... However, I saw somebody is using constraints = none and I was wandering why... Would somebody take the pleasure to embark on the discussion of such an issue with me? Thnx in advance, Nicola -- Nicola Staffolani PhD Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics> Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- 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.
