Dear all, I am a bit confused about [ dihedral constraints ].
I was planning to contraint a dihedral in a "flat-bottom" way, so that e.g. angles between 120 and 240 deg are sampled, but above 240 and below 140 are basically "not allowed". In other words, I just want a harmonic potential, where the point of zero-potential is stretched from a point Theta_0 to a range of Theta_0 +- delta_Theta. Dihedral restraints seemed to be what I need, at first glance, but I am confused about the resulting potential obtained from equation 12 in the manual: http://manual.gromacs.org/current/reference-manual/functions/restraints.html#dihedralrestraint The conditions - |Theta'| > delta_Theta - |Theta'| <= delta_Theta and the "(Theta' - delta_Theta)" in the first condition of eq. 12 will do it in an asymmetric way, with different behaviour at Theta' = + delta_Theta or Theta' = - delta_Theta. Therefore, is equation 12 just written in a strange way and it creates a symmetric flat-bottomed potential or will it really result in such an asymmetry? Thanks already for your help. Best wishes, Jacek ________________________________________________ Dr. Jacek Kozuch Freie Universität Berlin Fachbereich Physik Arnimallee 14 Raum 1.1.35 14 195 Berlin ________________________________________________ -- 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.
