Thank you very much for this quick answer!! Eva > > > On 6/13/12 7:55 AM, [email protected] wrote: >> 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. > > With restraints on heavy atoms, your positions will not deviate very much > at > all. A 1 Angstrom movement would be huge in this case; I would expect > your > deviations to be orders of magnitude less. > >> We need to minimize, simulate, minimize, simulate the hydrogen atoms. > > I don't follow the logic here. You say you need to do an EM of the H > atoms in > order to do some PBSA calculation with no MD, but here you're doing two > iterations of EM and MD. > >> 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: >> > > There are several problems here, most of which I've already stated, but > I'll > recapitulate them again. > >> >> define = -DPOSRES >> constraints = all-bonds >> integrator = steep >> nsteps = 30000 >> vdwtype = cutoff >> coulombtype = cutoff > > As Mark said, these settings should be "cut-off" not "cutoff." > >> epsilon_rf = 0 >> pbc = xyz > > For an implicit system, periodicity should be set to "no" and grompp will > warn > you about using angular COM removal (invoked below) if you leave it set as > is. > >> nstlist = 1 >> ns_type = grid >> rlist = 1 >> rcoulomb = 1.2 >> rvdw = 1.2 > > Finite cutoffs with implicit solvent will lead to instability and poor > energy > conservation. These three lines (rlist, rcoulomb, rvdw) should be set to > zero, > unless you're satisfied with artifacts. > >> rvdw_switch = 0.7 > > This setting has no effect when using cutoffs. > >> comm-mode = angular >> comm-grps = System >> nstcgsteep = 1000 >> emtol = 5.0 > > Unless you've compiled with double precision, it is unlikely you will > achieve a > minimal force this low. The use of restraints is going to preclude most > movement in the system, so don't be surprised if grompp does not (and > cannot) > achieve this tolerance. > >> emstep = 0.01 >> implicit_solvent = GBSA >> gb_algorithm = HCT >> nstgbradii = 1 >> rgbradii = 1 > > This should also be set to zero if the above neighbor searching parameters > are zero. > >> 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? >> > > Because settings like PME don't make sense for implicit solvent > calculations. > Plain cutoffs with finite values are almost never adequate for any > purpose, however. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 [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 >
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