I've been having problems getting implicit solvent systems (which are probably fairly experiment still in gromacs) to work correctly. I've been modelling a protein of about 11000 atoms with hydrogens in a 2 ns simulation. By the end of the simulation, the temperature has risen from 300 K to 496 K - and the protein unfolds. It was supposed to maintain temp at 300 K.
I have an a non-zero total charge of -6.999999. With explicit solvent, I would normally add the appropriate matching ions, but with implicit solvent what should you do? Could the non-zero total charge result in heating? Or is the thermostat not working well enough (should I change tau-t or ref-t?) Here is my md.mdp file: constraints = all-bonds ; trying.. integrator = md dt = 0.002 ; ps ! nsteps = 1000000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = cut-off fourierspacing = 0.16 vdwtype = cut-off rcoulomb = 1.0 rvdw = 1.0 ; important for neighbor searching pbc = no ; no periodic boundary conditions epsilon_rf = 0 rgbradii = 1.0 ; must equal rlist, rcoulomb, rvdw comm_mode = angular optimize_fft = yes implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80 sa_surface_tension = 2.25936 nstcomm = 10 nstxout = 1000 nstxtcout = 1000 nstvout = 0 nstfout = 0 tcoupl = andersen tc-grps = system tau-t = 0.1 ref-t = 300 gen_vel = yes gen_temp = 300 gen_seed = -1 ----- -- 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
