[gmx-users] large error bars in PMF

Rebeca García Fandiño regafan at hotmail.com
Fri Jul 22 12:15:27 CEST 2011


Hi again,
I have one doub about the suggestion of using a dodecahedral box for my umbrella sampling to remove the problems I am having with the peptides rotating. I cannot see why a dodecaheral box is going to avoid this. Would it be better a truncated octahedron?
Thanks a lot 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
> >  > > 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
> >  >
> >  > ========================================
> >  > --
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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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