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 I will appreciate your help, Steven On Tue, Aug 21, 2012 at 3:27 PM, Justin Lemkul <[email protected]> wrote: > > > On 8/21/12 10:23 AM, Steven Neumann wrote: >> >> On Tue, Aug 21, 2012 at 3:07 PM, Justin Lemkul <[email protected]> wrote: >>> >>> >>> >>> On 8/21/12 9:36 AM, Steven Neumann wrote: >>>> >>>> >>>> Dear Gmx Users, >>>> >>>> I got confused about reading free energy difference from PMF curve. >>>> It is the difference between maximum value on PMF curve (plateau - >>>> final state) and the starting point corresponding to minima. >>>> >>>> So e.g. my curve starts at 0 [kcal/mol] going staright to minima of -2 >>>> kcal/mol and then increase obtaining plateau of 14 kcal/mol. DeltaG = >>>> -16 kcal/mol or -12 kcal/mol ? >>>> >>> >>> It seems that your system has discovered a more energetically favorable >>> location where the minimum is at -2 kcal/mol. It should not be assumed >>> that >>> whatever arbitrary "start" point we choose is the energy minimum. In >>> your >>> case, it is not. DeltaG is the difference between final and initial >>> states. >>> Only you know what these states are. >>> >>> -Justin >> >> >> Thank you. Ok - mu curve starts at 0 kcal/mol corresponding to the >> reaction coordinate of 0.5 nm. going to -2 kcal mol at 0.6 nm then >> increasing as I said before to plateau of 14 kcal/mol. >> >> My first window (shown by grompp) corresponds to 0.8 nm of the >> reaction coordinate... So the initial state should be at 0.8 nm which >> corresponds to 0.5 kcal/mol or always take the initial state as >> initial of the curve? >> > > That depends on how you've set up your .mdp files. If you're telling a > configuration in which the groups are separated by 0.8 nm that they should > be separated by 0.5 nm instead, you need to allow for some time for that to > adjust. The restraint distances are what you tell them to be. Your initial > configurations should be as close to that COM separation as possible. > > So, the answer is, I don't have an answer, because you didn't provide an > .mdp file. > > -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 > * 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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. 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