[gmx-users] deltaG from PMF
Steven Neumann
s.neumann08 at gmail.com
Tue Aug 21 18:46:31 CEST 2012
Thanks Thomas.
Justin, could you please comment on this?
Steven
On Tue, Aug 21, 2012 at 5:37 PM, Thomas Schlesier <schlesi at uni-mainz.de> wrote:
> Am 21.08.2012 18:22, schrieb gmx-users-request at gromacs.org:
>>
>> On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesier<schlesi at 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-request at gromacs.org:
>>> >
>>>>
>>>> >>On Tue, Aug 21, 2012 at 4:21 PM, Justin Lemkul<jalemkul at vt.edu>
>>>> >> wrote:
>>>>>
>>>>> >>>
>>>>>>
>>>>>> >>> >
>>>>>> >>> >
>>>>>> >>> >On 8/21/12 11:18 AM, Steven Neumann wrote:
>>>>>> >>>>
>>>>>>>>
>>>>>>>> >>>> >>
>>>>>>>> >>>> >>On Tue, Aug 21, 2012 at 4:13 PM, Justin
>>>>>>>> >>>> >> Lemkul<jalemkul at vt.edu>
>>>>>>>> >>>> >>wrote:
>>>>>>>
>>>>>>> >>>>>
>>>>>>>>>>
>>>>>>>>>> >>>>> >>>
>>>>>>>>>> >>>>> >>>
>>>>>>>>>> >>>>> >>>
>>>>>>>>>> >>>>> >>>On 8/21/12 11:09 AM, Steven Neumann wrote:
>>>>>>>>
>>>>>>>> >>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> >>>>>> >>>>
>>>>>>>>>>>> >>>>>> >>>>
>>>>>>>>>>>> >>>>>> >>>>On Tue, Aug 21, 2012 at 3:48 PM, Justin
>>>>>>>>>>>> >>>>>> >>>> Lemkul<jalemkul at 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
>>>> >>
>>>>>>
>>>>>> >>> >
>>>>>> >>> >--
>>>
>>> >
>>> >
>>> >--
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>
>
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