Thanks for your answer.
My peptide has 6 residues and it is cyclic.
I calculated the errors through bootstrap, using this:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500 -n
Bootstrap 200
Are the pmfs aligned on the minimum distance value? Is that the value by
default? How could I calculate the errors based on the PMFs aligned on the long
distance value?
Thanks a lot for all the help.
Best wishes,
Rebeca.
> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
> Date: Thu, 21 Jul 2011 14:33:28 -0600
>
>
> One potential problem you have is that as Justin mentioned your minimum
> is not well defined and certain much less well sampled than the long
> distances
> windows. Small peptides (depends the size) may sample relevant phase
> space to get reasonable convergence within 8 ns when free in solution;
> in contact certainly not ...
>
> How long is you peptide?
>
> You might get a better estimate of your error by plotting all the pmfs
> you've
> got through bootstrap (if this is the case) ... and get the errors
> based on the
> pmfs aligned on the long distance value and not on the "minimum" which
> is
> probably what you did ... if the minimum is not well defined then it
> does not
> make sense.
>
> On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote:
>
> >
> >
> > Rebeca García Fandiño wrote:
> >> OK,
> >> I will try a dodecahedral box and also to extend my actual
> >> simulations.
> >> Could you give me some advice about starting to learn about 3D PMF?
> >> I have not seen this in the manual, and I have never used it
> >> before. I have only found your tutorial about how to calculate PMF
> >> in Gromacs 4...
> >
> > In practice, there's basically nothing different between 3D and 1D.
> > You specify the dimensions to which the biasing potential is applied
> > with pull_dim or pull_vec (depending on the pull_geometry used).
> > Right now you're calculating the PMF along the z-dimension only
> > ("pull_dim = N N Y"), which may be appropriate for one-dimensional
> > processes or those in which the reference group does not rotate much
> > in the timeframe of the sampling. Setting "pull_dim = Y Y Y" will
> > apply the restraint in all dimensions.
> >
> > -Justin
> >
> >> Thanks a lot again for your help.
> >> Best wishes,
> >> Rebeca.
> >> > Date: Thu, 21 Jul 2011 15:16:52 -0400
> >> > From: jalem...@vt.edu
> >> > To: gmx-users@gromacs.org
> >> > Subject: Re: FW: [gmx-users] large error bars in PMF
> >> >
> >> >
> >> >
> >> > Rebeca García Fandiño wrote:
> >> > >
> >> > >
> >> > > I am trying to achieve the binding energy of the dimer composed
> >> by the
> >> > > two small cyclic peptides, to compare it with experimental. What
> >> > > advantages would I have using 3D PMF instead only 1D for this
> >> calculation?
> >> >
> >> > Intuitively, two molecules diffuse through solution until they
> >> find one another,
> >> > which to me sounds a lot like a 3D path. Further, using a
> >> dodecahedral box for
> >> > your umbrella sampling removes the problems you're having with
> >> the peptides
> >> > rotating. It sounds like you're trying to pull in one direction
> >> along a
> >> > rectangular box, but the peptides are not playing nice. I feel
> >> like this
> >> > discussion has come up at least once or twice before, though...
> >> >
> >> > -Justin
> >> >
> >> > > Thanks a lot!
> >> > > Rebeca.
> >> > >
> >> > > > Date: Thu, 21 Jul 2011 14:14:44 -0400
> >> > > > From: jalem...@vt.edu
> >> > > > To: gmx-users@gromacs.org
> >> > > > Subject: Re: [gmx-users] large error bars in PMF
> >> > > >
> >> > > >
> >> > > >
> >> > > > Rebeca García Fandiño wrote:
> >> > > > > Hi,
> >> > > > > thanks a lot for your quick answer.
> >> > > > > What I am trying to pull are two small peptides one from
> >> another (r_1
> >> > > > > and r_2).
> >> > > > > I did not understand very well your last suggestion: "...if
> >> you want
> >> > > > > reasonable error bars you will not lots of well-converged
> >> data".
> >> > > >
> >> > > > Oops, that should have read "you will *need* lots of well-
> >> converged
> >> > > data."
> >> > > >
> >> > > > > Do you mean I will need also more windows besides extending
> >> the
> >> > > simulations?
> >> > > >
> >> > > > I doubt you need more windows. Likely you just need more time
> >> in each.
> >> > > >
> >> > > > > I think the problem could be also that the peptides I am
> >> using
> >> > > rotate in
> >> > > > > the box and they do not remain flat one respect to the
> >> other. They
> >> > > > > gyrate freely and some parts of their structure interact
> >> along the
> >> > > > > pulling...
> >> > > >
> >> > > > Interactions are part of the dissociation process and are not
> >> > > problematic per
> >> > > > se. But if you're trying to obtain only a one-dimensional PMF
> >> then your
> >> > > > rotation could be a problem. Is there some reason you need a
> >> > > one-dimensional
> >> > > > PMF and not a three-dimensional PMF? What are you trying to
> >> achieve?
> >> > > >
> >> > > > -Justin
> >> > > >
> >> > > > > Thanks a lot again for your help.
> >> > > > > Best wishes,
> >> > > > > Rebeca.
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > >
> >> > >
> >> ------------------------------------------------------------------------
> >> > > > > From: rega...@hotmail.com
> >> > > > > To: gmx-users@gromacs.org
> >> > > > > Date: Thu, 21 Jul 2011 16:36:59 +0000
> >> > > > > Subject: [gmx-users] large error bars in PMF
> >> > > > >
> >> > > > >
> >> > > > > Hi,
> >> > > > > I am trying to calculate the binding energy of two
> >> molecules using the
> >> > > > > PMF (Umbrella Sampling method) and Gromacs 4.0.
> >> > > > > Some weeks ago I have written to the list because changing
> >> the
> >> > > number of
> >> > > > > windows used in the Umbrella Sampling calculations
> >> different results
> >> > > > > were obtained, and I was suggested to extend my simulations
> >> since the
> >> > > > > error bars associated to each windows were too high.
> >> > > > > I have now extended my simulations from 1 ns to 8 ns,
> >> however, I
> >> > > cannot
> >> > > > > see much different from the shorter calculations. I send
> >> you the
> >> > > > > comparison of the two PMF including the error bars
> >> (attached).
> >> > > > > Now I am using 50 windows, but the shorter simulations were
> >> done using
> >> > > > > 100 windows, so I don't think increasing the number of
> >> windows
> >> > > could help.
> >> > > > > My system has about 29200 atoms (where 29000 are chloroform
> >> atoms).
> >> > > The
> >> > > > > *mdp file I am using is copied below.
> >> > > > > Would you have any suggestion to improve the results and
> >> decrease the
> >> > > > > error bars in the calculations?
> >> > > > >
> >> > > > > ----------------------------MDP
> >> file---------------------------
> >> > > > > title = Umbrella pulling simulation
> >> > > > > define =
> >> > > > > define =
> >> > > > > ; Run parameters
> >> > > > > integrator = md
> >> > > > > dt = 0.002
> >> > > > > tinit = 0
> >> > > > > nsteps = 500000 ; 1 ns
> >> > > > > nstcomm = 10
> >> > > > > ; Output parameters
> >> > > > > nstxout = 5000 ; every 10 ps
> >> > > > > nstvout = 5000
> >> > > > > nstfout = 5000
> >> > > > > nstxtcout = 5000 ; every 10 ps
> >> > > > > nstenergy = 5000
> >> > > > > ; Bond parameters
> >> > > > > constraint_algorithm = lincs
> >> > > > > constraints = all-bonds
> >> > > > > continuation = yes
> >> > > > > ; Single-range cutoff scheme
> >> > > > > nstlist = 5
> >> > > > > ns_type = grid
> >> > > > > rlist = 1.4
> >> > > > > rcoulomb = 1.4
> >> > > > > rvdw = 1.4
> >> > > > > ; PME electrostatics parameters
> >> > > > > coulombtype = PME
> >> > > > > fourierspacing = 0.12
> >> > > > > fourier_nx = 0
> >> > > > > fourier_ny = 0
> >> > > > > fourier_nz = 0
> >> > > > > pme_order = 4
> >> > > > > ewald_rtol = 1e-5
> >> > > > > optimize_fft = yes
> >> > > > > ; Berendsen temperature coupling is on in two groups
> >> > > > > Tcoupl = Nose-Hoover
> >> > > > > tc_grps = ACH CL3
> >> > > > > tau_t = 0.5 0.5
> >> > > > > ref_t = 300 300
> >> > > > > ; Pressure coupling is on
> >> > > > > Pcoupl = Parrinello-Rahman
> >> > > > > pcoupltype = isotropic
> >> > > > > tau_p = 1.0
> >> > > > > compressibility = 4.5e-5
> >> > > > > ref_p = 1.0
> >> > > > > ; Generate velocities is off
> >> > > > > gen_vel = no
> >> > > > > ; Periodic boundary conditions are on in all directions
> >> > > > > pbc = xyz
> >> > > > > ; Long-range dispersion correction
> >> > > > > DispCorr = EnerPres
> >> > > > > ; Pull code
> >> > > > > pull = umbrella
> >> > > > > pull_geometry = distance
> >> > > > > pull_dim = N N Y
> >> > > > > pull_start = yes
> >> > > > > pull_ngroups = 1
> >> > > > > pull_group0 = r_1
> >> > > > > pull_group1 = r_2
> >> > > > > pull_init1 = 0
> >> > > > > pull_rate1 = 0.0
> >> > > > > pull_k1 = 1000 ; kJ mol^-1 nm^-2
> >> > > > > pull_nstxout = 1000 ; every 2 ps
> >> > > > > pull_nstfout = 1000 ; every 2 ps
> >> > > > >
> >> > > > > -----------------------------------------------
> >> > > > >
> >> > > > >
> >> > > > > Thanks a lot in advance.
> >> > > > >
> >> > > > > Best wishes,
> >> > > > >
> >> > > > > Dr. Rebeca Garcia
> >> > > > > Santiago de Compostela University
> >> > > > > Spain
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > > -- gmx-users mailing list gmx-users@gromacs.org
> >> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users Please
> >> search the
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> >> > > > >
> >> > > >
> >> > > > --
> >> > > > ========================================
> >> > > >
> >> > > > Justin A. Lemkul
> >> > > > Ph.D. Candidate
> >> > > > ICTAS Doctoral Scholar
> >> > > > MILES-IGERT Trainee
> >> > > > Department of Biochemistry
> >> > > > Virginia Tech
> >> > > > Blacksburg, VA
> >> > > > jalemkul[at]vt.edu | (540) 231-9080
> >> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >> > > >
> >> > > > ========================================
> >> > > > --
> >> > > > gmx-users mailing list gmx-users@gromacs.org
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> >> > >
> >> >
> >> > --
> >> > ========================================
> >> >
> >> > Justin A. Lemkul
> >> > Ph.D. Candidate
> >> > ICTAS Doctoral Scholar
> >> > MILES-IGERT Trainee
> >> > 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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> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > 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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