On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > > >> >> On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Steven Neumann wrote: >> >> I run energy minimization of my protein with implicit solvent: >> constraints = none >> >> integrator = steep >> >> dt = 0.001 ; ps >> >> nsteps = 30000 >> >> vdwtype = cut-off >> >> coulombtype = cut-off >> >> pbc = no >> >> nstlist = 0 >> >> ns_type = simple >> >> rlist = 0 ; this means all-vs-all (no cut-off), >> >> which gets expensive for bigger systems >> >> rcoulomb = 0 >> >> rvdw = 0 >> >> comm-mode = angular >> >> comm-grps = Protein >> >> optimize_fft = yes >> >> ; >> >> ; Energy minimizing stuff >> >> ; >> >> emtol = >> >> 5.0 >> >> emstep = 0.01 >> >> ; >> >> ; Implicit solvent >> >> ; >> >> implicit_solvent = GBSA >> >> gb_algorithm = OBC >> >> nstgbradii = 1 >> >> rgbradii = 0 ; [nm] Cut-off for the calculation of the >> >> Born radii. Currently must be equal to rlist >> >> gb_epsilon_solvent = 80 ; Dielectric constant for the >> implicit solvent >> >> ; gb_saltconc = 0 ; Salt concentration for implicit solvent >> >> models, currently not used >> >> sa_algorithm = Ace-approximation >> >> sa_surface_tension = 2.25936 >> >> And I obtained: >> Steepest Descents: >> >> Tolerance (Fmax) = 1.00000e+03 >> >> Number of steps = 30000 >> >> Step Time Lambda >> >> 0 0.00000 0.00000 >> >> >> >> Steepest Descents converged to Fmax < 1000 in 1 steps >> >> Potential Energy = inf >> >> Maximum force = 0.0000000e+00 on atom 0 >> >> Norm of force = nan >> >> Can you please explain? >> >> >> Not without more information. >> >> 1. What is in the system? - protein without specified box >> 2. Which version of Gromacs is this? - Gromacs 4.5.4 >> 3. Are you using GPU or CPU architecture? - I run it straight from >> the cluster on a specific node >> > > Doesn't answer the question, but I'll assume CPU since EM doesn't work on > GPU's. Just checking. > > > 4. Does an in vacuo minimization work (i.e., just turn off the GB >> parts)? - yes, it works >> >> > And what is the output? > > In any case, I can't reproduce any problem doing EM with implicit solvent > in 4.5.4 - my test systems work quite well. It may just be that the system > cannot be minimized because of some clash that is unfavorable in an > implicit solvent environment (thus causing an immediate halt, though that > would be odd) but can be resolved in vacuo. Try using the structure > produced by in vacuo minimization as input into the implicit solvent EM to > see if this may be the case. > > > >> What shoould be the value for emtol in implicit solvent model with >> protein with app. 150 residues? >> >> > One that is sufficient for the inherent forces in the system and for your > application ;) I don't think there are any hard and fast rules here for > standard MD, and the target is not dictated by the size of the protein. > > > -Justin > Thank you Justin. Mark, would you suggest equilibration e.g. for 1ns with no restraints and no constraints in implicic solvent with timestep =0.0005 and then run MD with implicit employing LINCS? Steven > > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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