I did g_wham calculation as you suggested for: 10-30 ns 30-50 ns 10-50 ns In some cases of PMF curves the drift is 0.3 kcal/mol but in some cases it is over 1.5 kcal/mol so huge drifts. In terms of huge drifts what would you suggest ?
Steven On Tue, Aug 21, 2012 at 5:48 PM, Justin Lemkul <[email protected]> wrote: > > > On 8/21/12 12:46 PM, Steven Neumann wrote: >> >> Thanks Thomas. >> Justin, could you please comment on this? >> > > I agree with everything Thomas has said. There's not really anything to > say. > > -Justin > > >> Steven >> >> On Tue, Aug 21, 2012 at 5:37 PM, Thomas Schlesier <[email protected]> >> wrote: >>> >>> Am 21.08.2012 18:22, schrieb [email protected]: >>>> >>>> >>>> On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesier<[email protected]> >>>> wrote: >>>>> >>>>> >>>>>> Since your simulations of the individual windows are about 50 ns, you >>>>>> could >>>>>> first dismiss the first 10 ns for equilibration, and then perform the >>>>>> WHAM >>>>>> analysis for 10-30 ns and 30-50 ns. If everything is fine, you should >>>>>> see no >>>>>> drift. >>>>>> If you want to have more data for the analysis you could also use 5ns >>>>>> ; >>>>>> 5-27.5ns and 27.5-50ns. >>>>>> >>>>>> From the PMF it seems that the equilibrium state should be around 0.6 >>>>>> nm. To >>>>>> be sure, you can perform a normal simulation (without any restraints) >>>>>> from >>>>>> you initial starting window (~0.4nm) and a window near the minima >>>>>> (~0.6nm). >>>>>> Then after the equilibration phase, look at the distribution of the >>>>>> distance >>>>>> along the reaction coordinate. If in both cases the maximum is at >>>>>> ~0.6nm, >>>>>> this should be the 'true' equilibrium state of the system (instead of >>>>>> the >>>>>> first window of the PMF calculation) and i would measure \Delta G from >>>>>> this >>>>>> point. >>>>>> >>>>>> Greetings >>>>>> Thomas >>>> >>>> >>>> >>>> >>>> Thanks Thomas for this but finally I realised that my first >>>> configuration corresponds to 0.6 nm which is the minima so I take the >>>> free energy difference based on this value and plateau. >>>> >>>> I want also to calculate error bars. Would you do this: >>>> >>>> Final PMF curve for 10-50 ns >>>> >>>> Error bars from: >>>> g_wham -b 30000 -e 40000 >>>> >>>> g_wham -b 50000 -e 60000 >>>> >>> >>> Think this approach would be good to see if you have any drifts. >>> But for error bars there is something implemented in 'g_wham'. But i >>> never >>> used it, since for my system umbrella sampling is not really applicable, >>> only TI. So i can't comment on it, if there is anything one should be >>> aware >>> of, or similar. But 'g_wham -h' prints some info about how to use the >>> error >>> analysis >>> Greetings >>> Thomas >>> >>> >>> >>>> >>>> >>>> Steven >>>> >>>> >>>>>> >>>>>> >>>>>> Am 21.08.2012 17:25, [email protected]: >>>>>> >>>>>> >>>>>>>> On Tue, Aug 21, 2012 at 4:21 PM, Justin Lemkul<[email protected]> >>>>>>>> wrote: >>>>>>> >>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 8/21/12 11:18 AM, Steven Neumann wrote: >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Tue, Aug 21, 2012 at 4:13 PM, Justin >>>>>>>>>>>>>>>> Lemkul<[email protected]> >>>>>>>>>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On 8/21/12 11:09 AM, Steven Neumann wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 21, 2012 at 3:48 PM, Justin >>>>>>>>>>>>>>>>>>>>>>>> Lemkul<[email protected]> >>>>>>>>>>>>>>>>>>>>>>>> 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? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Based on the very little information I have, no. It >>>>>>>>>>>>>>>>>>>> would appear >>>>>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>> 0.4 nm separation is in fact some metastable state and >>>>>>>>>>>>>>>>>>>> the true >>>>>>>>>>>>>>>>>>>> energy >>>>>>>>>>>>>>>>>>>> minimum is at 0.6 nm of COM separation. What's going on >>>>>>>>>>>>>>>>>>>> at that >>>>>>>>>>>>>>>>>>>> location? >>>>>>>> >>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> My mistake. The initial grompp of 1st configuartion (where >>>>>>>>>>>>>>>> ligand >>>>>>>>>>>>>>>> stakced on keratin surface) corresponds to 0.6 nm where >>>>>>>>>>>>>>>> is the minimum. Thus deltaG would be -7.22 kcal/mol. Am I >>>>>>>>>>>>>>>> right? Or >>>>>>>>>>>>>>>> Shall I take difference between 0 and 5.22 ? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -7.22 kcal/mol sounds much more logical to me. If your first >>>>>>>>>>>> configuration >>>>>>>>>>>> is at the energy minimum, that's not something you ignore. The >>>>>>>>>>>> zero >>>>>>>>>>>> point >>>>>>>>>>>> can be set wherever you like with the g_wham flag -zprof0, so >>>>>>>>>>>> it's >>>>>>>>>>>> really >>>>>>>>>>>> rather arbitrary. The WHAM algorithm simply sets the leftmost >>>>>>>>>>>> window >>>>>>>>>>>> (smallest value along the reaction coordinate) to zero to >>>>>>>>>>>> construct the >>>>>>>>>>>> remainder of the PMF curve. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 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. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> That seems fairly short, especially given the generation >>>>>>>>>>>>>>>>>>>> of >>>>>>>>>>>>>>>>>>>> velocities in >>>>>>>>>>>>>>>>>>>> conjunction with the Parrinello-Rahman barostat, which >>>>>>>>>>>>>>>>>>>> can be very >>>>>>>>>>>>>>>>>>>> temperamental. >>>>>>>> >>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Would you suggest e.g. skip 1 ns? >>>>>>>>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> I'm not going to make an arbitrary guess. It's up to you to >>>>>>>>>>>> analyze the >>>>>>>>>>>> timeframe required for whatever relevant observables to >>>>>>>>>>>> converge. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -Justin >>>>>> >>>>>> >>>>>>>> >>>>>>>> Thanks for this. >>>>>>>> >>>>>>>> Steven >>>>>>>> >>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>> >>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> gmx-users mailing [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 [email protected]. >>>>>> * Can't post? Readhttp://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. Use the www >>> interface or send it to [email protected]. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ======================================== > > 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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