[gmx-users] deltaG from PMF
Steven Neumann
s.neumann08 at gmail.com
Fri Aug 24 14:58:52 CEST 2012
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 <jalemkul at vt.edu> 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 <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
>>>>>>>>
>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>
>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> gmx-users mailing listgmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> * Only plain text messages are allowed!
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>>>
>>>
>>>
>>> --
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>
>
> --
> ========================================
>
> 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
>
> ========================================
>
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