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
 > > archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
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 > > www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
 > > Read http://www.gromacs.org/Support/Mailing_Lists
 > >
 >
 > --
 > ========================================
 >
 > 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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