Hi There has been a number of reports lately about ill-behaving simulations using implicit solvent. I'm currently trying to investigate the cause of this, as such simulations used to work very nice in our hands.
In the meantime I would advice to use implicit solvent with caution. Thanks /Per Skickat från min iPhone 30 okt 2011 kl. 02:10 skrev Matt Larson <larsonma...@gmail.com>: > 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 -- 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
