[gmx-users] large error bars in PMF
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 21 21:36:35 CEST 2011
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: jalemkul at vt.edu
> > To: gmx-users at 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: jalemkul at vt.edu
> > > > To: gmx-users at 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: regafan at hotmail.com
> > > > > To: gmx-users at 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 at 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
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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