Hi! Thank you for your answer. > On 13/06/2012 6:44 PM, [email protected] wrote: >> Hi everybody, >> I want to do a minimization of the hydrogens of my protein. Only the >> hydrogens. > > Doesn't really matter - nothing will move more than a fraction of an > Angstrom unless it's horribly wrong, in which case not moving the heavy > atoms won't help you. > >> And I want to do this with implicit solvent. > > Probably not worth the effort if you're just preparing for MD.
Our goal is not an MD simulation of the protein. We plan a Poisson-Boltzmann electrostatics calculation. For that we need the heavy atoms as they are in the crystal structure (even 1 Angstroem movement would be too much) with good hydrogen atom position. We need to minimize, simulate, minimize, simulate the hydrogen atoms. Implicit solvent is ok for us. (For a later MD run of the complete protein, we will use explicit solvent). This is the .mdp file: define = -DPOSRES constraints = all-bonds integrator = steep nsteps = 30000 vdwtype = cutoff coulombtype = cutoff epsilon_rf = 0 pbc = xyz nstlist = 1 ns_type = grid rlist = 1 rcoulomb = 1.2 rvdw = 1.2 rvdw_switch = 0.7 comm-mode = angular comm-grps = System nstcgsteep = 1000 emtol = 5.0 emstep = 0.01 implicit_solvent = GBSA gb_algorithm = HCT nstgbradii = 1 rgbradii = 1 gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm = Ace-approximation sa_surface_tension = -1 Additionally I have a question according to the vdwtype and coulombtype. Why do I have to set the two parameters to cutoff? Eva > >> All the time when I try it there are errors in my .mdp file. Can you >> please give me an example how such a .mdp file should look like. > > Every tutorial you've done will have an example EM .mdp file. Searching > Google for some implicit solvent examples will provide some leads. > Ultimately you need to learn how to create and manage one, so hoping one > will appear and using it blindly is not terribly productive. > > Mark > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
