Hi Micheal, Just to make sure I understand you correctly -- I can have 1 type of restraint, e.g., a harmonic potential between 2 groups defined by (k1, d1) where k1 is force constant and d1 is the equilibrium position. But I can't have 2 or more types of restraints like (k1,d1,k2,d2,...,kn,dn). Is that correct?
Also, about to paper you referred to. Is the algorithm described in section IIIB-2 the one that's currently implemented in gromacs? If so, how do you "precompute" the matrix U for all pairs without knowing x? I guess I just don't have an idea about how the whole procedure is conducted. Thanks, Dejun -- View this message in context: http://gromacs.5086.n6.nabble.com/Hamiltonian-replica-exchange-umbrella-sampling-with-gmx-4-6-tp5006187p5006853.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
