On Thu, Mar 8, 2012 at 2:18 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> Dear Gmx Users, Dear Justin, >> I pulled my ligand away from my protein. Ligand was attached to lower >> part of my protein, I pulled in Z coordinate it using: >> >> ; Run parameters >> >> integrator = md ; leap-frog integrator >> >> nsteps = 5000000 ; 2 * 5000000 = 10 ns >> >> dt = 0.002 ; 2 fs >> >> tinit = 0 >> >> nstcomm = 10 >> >> ; Output control >> >> nstxout = 50000 ; save coordinates every 100 ps >> >> nstvout = 50000 ; save velocities every >> >> nstfout = 5000 >> >> nstxtcout = 5000 ; every 10 ps >> >> nstenergy = 5000 >> >> ; Bond parameters >> >> continuation = yes ; first dynamics run >> >> constraint_algorithm = lincs ; holonomic constraints >> >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained >> >> ; Neighborsearching >> >> ns_type = grid ; search neighboring grid cells >> >> nstlist = 5 ; 10 fs >> >> rlist = 0.9 ; short-range neighborlist cutoff (in nm) >> >> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) >> >> rvdw = 0.9 ; short-range van der Waals cutoff (in nm) >> >> ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential >> rcoulomb >> >> ; Electrostatics >> >> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics >> >> pme_order = 4 ; cubic interpolation >> >> fourierspacing = 0.12 ; grid spacing for FFT >> >> fourier_nx = 0 >> >> fourier_ny = 0 >> >> fourier_nz = 0 >> >> 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 ; pressure coupling is on for NPT >> >> pcoupltype = isotropic ; uniform scaling of box vectors >> >> tau_p = 1.0 ; time constant, in ps >> >> ref_p = 1.0 ; reference pressure, in bar >> >> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 >> >> ; Periodic boundary conditions >> >> pbc = xyz ; 3-D PBC >> >> ; Dispersion correction >> >> DispCorr = EnerPres ; account for cut-off vdW scheme >> >> ; Velocity generation >> >> gen_vel = no ; assign velocities from Maxwell distribution >> >> ; These options remove COM motion of the system >> >> ; Pull code >> >> pull = umbrella >> >> pull_geometry = distance >> >> pull_dim = N N Y >> >> pull_start = yes >> >> pull_ngroups = 1 >> >> pull_group0 = Protein >> >> pull_group1 = LIG182 >> >> pull_init1 = 0 >> >> pull_rate1 = 0.0 >> >> pull_k1 = 200 ; kJ mol^-1 nm^-2 >> >> pull_nstxout = 1000 ; every 2 ps >> >> pull_nstfout = 1000 ; every 2 ps >> >> Following Justin's tutorial I used perl script to extract coordinate for >> each window. >> >> 0 2.4595039 >> >> 1 2.4745028 >> >> ... >> >> 500 8.74 >> >> My ligand at the begining was at such distance as it was in the lower >> part of the protein. Then I used 0.1 nm spacing at the begining (till 4 nm) >> and 0.2 nm later on. >> >> And following equilibration in each window I run umbrella sampling for >> 10ns in app 49 windows: >> >> Run parameters >> >> integrator = md ; leap-frog integrator >> >> nsteps = 5000000 ; 2 * 5000000 = 10 ns >> >> dt = 0.002 ; 2 fs >> >> tinit = 0 >> >> nstcomm = 10 >> >> ; Output control >> >> nstxout = 50000 ; save coordinates every 100 ps >> >> nstvout = 50000 ; save velocities every >> >> nstfout = 5000 >> >> nstxtcout = 5000 ; every 10 ps >> >> nstenergy = 5000 >> >> ; Bond parameters >> >> continuation = yes ; first dynamics run >> >> constraint_algorithm = lincs ; holonomic constraints >> >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained >> >> ; Neighborsearching >> >> ns_type = grid ; search neighboring grid cells >> >> nstlist = 5 ; 10 fs >> >> rlist = 0.9 ; short-range neighborlist cutoff (in nm) >> >> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) >> >> rvdw = 0.9 ; short-range van der Waals cutoff (in nm) >> >> ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential >> rcoulomb >> >> ; Electrostatics >> >> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics >> >> pme_order = 4 ; cubic interpolation >> >> fourierspacing = 0.12 ; grid spacing for FFT >> >> fourier_nx = 0 >> >> fourier_ny = 0 >> >> fourier_nz = 0 >> >> 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 ; pressure coupling is on for NPT >> >> pcoupltype = isotropic ; uniform scaling of box vectors >> >> tau_p = 1.0 ; time constant, in ps >> >> ref_p = 1.0 ; reference pressure, in bar >> >> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 >> >> ; Periodic boundary conditions >> >> pbc = xyz ; 3-D PBC >> >> ; Dispersion correction >> >> DispCorr = EnerPres ; account for cut-off vdW scheme >> >> ; Velocity generation >> >> gen_vel = no ; assign velocities from Maxwell distribution >> >> ; These options remove COM motion of the system >> >> ; Pull code >> >> pull = umbrella >> >> pull_geometry = distance >> >> pull_dim = N N Y >> >> pull_start = yes >> >> pull_ngroups = 1 >> >> pull_group0 = Protein >> >> pull_group1 = LIG182 >> >> pull_init1 = 0 >> >> pull_rate1 = 0.0 >> >> pull_k1 = 200 ; kJ mol^-1 nm^-2 >> >> pull_nstxout = 1000 ; every 2 ps >> >> pull_nstfout = 1000 ; every 2 ps >> >> >> My PMF profile: >> >> http://speedy.sh/zerqZ/**profile.JPG <http://speedy.sh/zerqZ/profile.JPG> >> >> My histogram: >> http://speedy.sh/PyhnN/Histo.**JPG<http://speedy.sh/PyhnN/Histo.JPG> >> >> Why g_wham takes into account distances below 2.45 nm as the 1st >> structure was at 2.45. If I get rid of the distances below 2.45 (those >> weird values PMF values) I obtain beautiful profile: >> >> http://speedy.sh/TUXGC/**profile1.JPG<http://speedy.sh/TUXGC/profile1.JPG> >> >> Please, explain! >> >> > The way you're thinking about distance is not consistent. Again, this is > a hazard of trying to map my tutorial onto your problem. You say you have > a ligand bound to the "lower part" of your protein, and then you're pulling > in the z-direction. The COM distance (as measured by g_dist and extracted > using my script) is not equivalent to the distance along the reaction > coordinate, if that reaction coordinate is only one dimension. In the > tutorial, it was. Here, it is not, hence the massive sampling defects that > you're observing and considerable redundancy in many of your windows. > > Check the output of grompp for the actual restraint distances that mdrun > will interpret. They are printed to the screen. > > -Justin > Thank you Justin!!! 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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