On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> Dear Justin and Gmx Users, >> >> I run a pulling of my ligand away from my protein with the same mdp file >> and I obtained two different plots - Force vs time (The breaking point >> occured at different times with different force). Can you please explain? >> > > If you change the stiffness of the spring, you change the magnitude of the > applied force. Thus, the behavior you see will occur either faster or > slower, depending on the strength of the spring. > > -Justin > > So how can I change the stiffness of my spring? Steven > > My mdp file: >> >> title = Umbrella pulling simulation >> define = -DPOSRES_L >> ; Run parameters >> integrator = md >> dt = 0.002 >> tinit = 0 >> nsteps = 250000 ; 0.5ns >> nstcomm = 10 >> ; Output parameters >> nstxout = 5000 ; every 10 ps >> nstvout = 5000 >> nstfout = 500 >> nstxtcout = 500 ; every 1 ps >> nstenergy = 500 >> ; Bond parameters >> constraint_algorithm = lincs >> constraints = all-bonds >> continuation = yes ; continuing from NPT >> ; Single-range cutoff scheme >> nstlist = 5 >> ns_type = grid >> rlist = 0.9 >> rcoulomb = 0.9 >> rvdw = 0.9 >> ; PME electrostatics parameters >> coulombtype = PME >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; Temperature coupling is on >> tcoupl = V-rescale ; modified Berendsen >> thermostat >> tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more >> accurate >> tau_t = 0.1 0.1 ; time constant, in ps >> ref_t = 298 298 ; reference temperature, one >> for each group, in K >> ; Pressure coupling is on >> Pcoupl = Parrinello-Rahman >> pcoupltype = isotropic >> tau_p = 1.0 compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Generate velocities is off >> gen_vel = no >> ; Periodic boundary conditions are on in all directions >> pbc = xyz >> ; Long-range dispersion correction >> DispCorr = EnerPres >> ; Pull code >> pull = umbrella >> pull_geometry = distance ; simple distance increase >> pull_dim = N N Y >> pull_start = yes ; define initial COM distance > 0 >> pull_ngroups = 1 >> pull_group0 = Protein >> pull_group1 = LIG182 >> pull_rate1 = 0.016 ; 0.008 nm per ps = 8 nm per ns >> pull_k1 = 200 ; kJ mol^-1 nm^-2 >> >> > -- > ==============================**========== > > 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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