On Thu, Dec 8, 2011 at 11:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > lina wrote: >> >> 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. >> > > You should not use PBC. Cutoffs should be infinite (i.e. all set to zero). Thanks, I noticed the example in the gromacs-gpubench-dhfr.tar.gz use PBC=no and Cut-off is infinite.
> I have never achieved stable simulations with finite cutoffs, even long > ones, in implicit solvent simulations. Thanks for reminding. > > The tcoupl setting is ignored when using the sd integrator, and there is > very little need to do any position restraining in implicit solvent > simulations, as there is no solvent to relax, you're just restraining the > protein and not accomplishing anything. gen_vel should be set to "yes" to > generate velocities following EM. Thanks again, I restrained some peptides, another peptides are free. hopefully it will work. > > -Justin > > >> 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 > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
