On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/21/12 10:42 AM, Steven Neumann wrote: >> >> Please see the example of the plot from US simulations and WHAM: >> >> http://speedy.sh/Ecr3A/PMF.JPG >> >> First grompp of frame 0 corresponds to 0.8 nm - this is what was shown >> by grompp at the end. >> >> The mdp file: >> >> ; Run parameters >> define = -DPOSRES_T >> integrator = md ; leap-frog integrator >> nsteps = 25000000 ; 100ns >> dt = 0.002 ; 2 fs >> tinit = 0 >> nstcomm = 10 >> ; Output control >> nstxout = 0 ; save coordinates every 100 ps >> nstvout = 0 ; save velocities every >> nstxtcout = 50000 ; every 10 ps >> nstenergy = 1000 >> ; Bond parameters >> continuation = no ; 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 >> vdwtype = Switch >> rvdw-switch = 1.0 >> rlist = 1.4 ; short-range neighborlist cutoff (in nm) >> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) >> rvdw = 1.2 ; 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 = 318 318 ; 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 = 2.0 ; 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 = yes ; assign velocities from Maxwell distribution >> gen_temp = 318 ; temperature for Maxwell distribution >> gen_seed = -1 ; generate a random seed >> ; 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 = LIG >> pull_init1 = 0 >> pull_rate1 = 0.0 >> pull_k1 = 500 ; kJ mol^-1 nm^-2 >> pull_nstxout = 1000 ; every 2 ps >> pull_nstfout = 1000 ; every 2 ps >> >> > > Based on these settings you're allowing grompp to set the reference distance > to whatever it finds in the coordinate file. It seems clear to me that the > sampling indicates what I said before - you have an energy minimum somewhere > other than where you "started" with. What that state corresponds to > relative to what you think is going on is for you to decide based on the > nature of your system. Whatever is occurring at 0.6 nm of COM separation is > of particular interest, since the energy minimum is so distinct. >
So based on this the deltaG will correspond to -5.22 as the initial state was taken at 0.4 nm corresponding to 0 kcal/mol as the moment corresponding to the minimum is the coordinate from SMD where last hydrogen bond was broken. Would you agree? > I hope you're doing a thorough analysis of convergence if you're generating > velocities at the outset of each run, and removing unequilibrated frames > from your analysis. When I use WHAM I skip first 200 ps of each window as the equilibration. Steven > > > -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 gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists