[gmx-users] deltaG from PMF

Steven Neumann s.neumann08 at gmail.com
Fri Aug 24 17:13:18 CEST 2012 

Thanks for this!

Steven

On Fri, Aug 24, 2012 at 3:26 PM, Thomas Schlesier <schlesi at uni-mainz.de> wrote:
> 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
>>>>>>>> >>>>>>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 ittogmx-users-request at gromacs.org.
>>>>>>>> >>>>>>* Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>>--
>>>>> >>>gmx-users mailing listgmx-users at 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-request at gromacs.org.
>>>>> >>>* Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists
>>>
>>> >
>
>
> --
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