[gmx-users] deltaG from PMF
Thomas Schlesier
schlesi at uni-mainz.de
Fri Aug 24 16:26:39 CEST 2012
As a first step, i would shift all curves so, that the energy of the
minium is for all plots at the same (aribarity) value. The minimum
should be the point which has sampled the best. If you shift then all
values, it should be easier to spot differences between the plots.
And probably make the analysis for every 10ns slices
10-20, 20-30, ...
then it's easier to see if you have a drift or fluctuations.
If you identify problematic regions you could do there additional
umbrella simulations, probably with higher force constants, in order to
sample that region better.
In theory the PMF should converge if you wait long enough, till the
system equilibrates under the external restraints (how long this takes?
nobody knows). On could probably wait a long time, big question here is
what is the biggest error you would tolerate. On the other hand one
can't simulate forever...
Look for what other people used for simulation-times for umbrella
sampling (i have the impression that 50ns is rather long, but i could
fool me here) and what they did to estimate if the calculations are
converged. Then decide, what to do.
Think nobody here would / will tell you this or this error is ok ... but
if you do something reasonable, which is in accord what others do / did
it should be ok.
Am 24.08.2012 14:59, schrieb gmx-users-request at gromacs.org:
> 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, schriebgmx-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 mailinglistgmx-users at gromacs.org
>>>>>>> >>>>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>> >>>>>>* Only plain text messages are allowed!
>>>>>>> >>>>>>* Please search the archive at
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>>>>>>> >>>>>>interface or send ittogmx-users-request at gromacs.org.
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>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>>--
>>>> >>>gmx-users mailing listgmx-users at gromacs.org
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>>>> >>>* Please search the archive at
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>> >
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