On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni <gianluca.sant...@ibs.fr> wrote: > Hi gmx_users, > is there any tutorial for implicit solvent simulation available?
Hi, I tried it few days ago. 1] pdb2gmx the water model choose none. 2] after editconf, go to energy minimization directly * It's important to relax the system well. 3] NVT 4] You may find one .mdp file from gromacs-gpubench-dhfr.tar.gz At bottom also attached the one I tried. If some part is wrong, please let me know. Thanks, define = -DPOSRES integrator = sd nsteps = 1000000000 dt = 0.0005 nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 continuation = yes constraints = all-bonds ns_type = grid nstlist = 1.0 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 coulombtype = Cut-off pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = A B C tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 pbc = xyz gen_vel = no ld_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii = 1.0 gb_epsilon_solvent = 80 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 0.0054 > > Thanks! > > -- > Gianluca Santoni, > Institut de Biologie Structurale > 41 rue Horowitz > Grenoble > _________________________________________________________ > Please avoid sending me Word or PowerPoint attachments. > See http://www.gnu.org/philosophy/no-word-attachments.html > > -- > 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
