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
>
> ========================================
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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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