Thanks Thomas. Justin, could you please comment on this? Steven
On Tue, Aug 21, 2012 at 5:37 PM, Thomas Schlesier <schl...@uni-mainz.de> wrote: > Am 21.08.2012 18:22, schrieb gmx-users-requ...@gromacs.org: >> >> On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesier<schl...@uni-mainz.de> >> 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, schriebgmx-users-requ...@gromacs.org: >>> > >>>> >>>> >>On Tue, Aug 21, 2012 at 4:21 PM, Justin Lemkul<jalem...@vt.edu> >>>> >> wrote: >>>>> >>>>> >>> >>>>>> >>>>>> >>> > >>>>>> >>> > >>>>>> >>> >On 8/21/12 11:18 AM, Steven Neumann wrote: >>>>>> >>>> >>>>>>>> >>>>>>>> >>>> >> >>>>>>>> >>>> >>On Tue, Aug 21, 2012 at 4:13 PM, Justin >>>>>>>> >>>> >> Lemkul<jalem...@vt.edu> >>>>>>>> >>>> >>wrote: >>>>>>> >>>>>>> >>>>> >>>>>>>>>> >>>>>>>>>> >>>>> >>> >>>>>>>>>> >>>>> >>> >>>>>>>>>> >>>>> >>> >>>>>>>>>> >>>>> >>>On 8/21/12 11:09 AM, Steven Neumann wrote: >>>>>>>> >>>>>>>> >>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>> >>>> >>>>>>>>>>>> >>>>>> >>>> >>>>>>>>>>>> >>>>>> >>>>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? >>>>>>>>>>>> >>>>>> >>>> >>>>>>> >>>>>>> >>>>> >>>>>>>>>> >>>>>>>>>> >>>>> >>> >>>>>>>>>> >>>>> >>>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 listgmx-us...@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 togmx-users-requ...@gromacs.org. >>> >* Can't post? 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