[gmx-users] large error bars in PMF
Rebeca García Fandiño
regafan at hotmail.com
Fri Jul 22 13:24:35 CEST 2011
Forget my last mail, I was not seeing the box correctly.
Sorry about that.
Best wishes,
Rebeca.
From: regafan at hotmail.com
To: jalemkul at vt.edu; gmx-users at gromacs.org
Subject: RE: [gmx-users] large error bars in PMF
Date: Fri, 22 Jul 2011 10:15:27 +0000
CC:
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
> > >
> > > ========================================
> > > --
> > > 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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