[gmx-users] boundaries in PMF
Justin A. Lemkul
jalemkul at vt.edu
Thu May 31 20:00:26 CEST 2012
On 5/31/12 1:58 PM, Rebeca García Fandiño wrote:
> Thanks again, and sorry for insisting, but I am not sure of understanding it
> totally.
> So, the boundaries g_wham calculates are not related to the dimensions of my
> channel? Would be any way to convert these units into the position of the ion in
> the channel in each case?
The pullx.xvg files contain helpful information in this case - the COM position
of the reference group and restrained group along the restrained dimension(s).
This should be what you're looking for, correct?
The WHAM algorithm doesn't care about the absolute position of anything, it's
the COM distance between the restrained and reference groups that matter. It's
that figure that should motivate how the windows were constructed and then analyzed.
-Justin
> Thanks again a lot for your help.
> Best wishes,
> Rebeca.
>
> > Date: Thu, 31 May 2012 13:45:18 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] boundaries in PMF
> >
> >
> >
> > On 5/31/12 1:38 PM, Rebeca García Fandiño wrote:
> > > Thanks a lot for your quick answer.
> > > The mdp file I have used is copied below. What is strange is that when I
> look at
> > > the *gro files for the different windows (100 windows in total), i. e:
> > >
> > > window 1: 8704Na Na56458 5.134 5.085 5.824
> > > window 50: 8704Na Na56458 5.053 5.081 3.459
> > > window 100: 8704Na Na56458 4.990 5.042 0.951
> > >
> > > you can see that the z-coordinate goes from 0.951 to 5.824 nm
> > >
> > > I should have a total distance in the x-axis of about 5 nm, and however, the
> > > boundaries calculated by g_wham are
> > >
> > > "Determined boundaries to 0.000035 to 2.603290 "
> > >
> > > Can you see anything in the mdp file which is causing this behaviour...?
> > >
> >
> > No, but you need to be careful how you're interpreting what you get. The
> > z-coordinate of your ion is not what's relevant; its displacement along the
> > z-axis from the reference group is what matters. So unless your reference group
> > is centered at z=0 (which it shouldn't, based on the way Gromacs builds boxes),
> > you won't have a range equivalent to the z-coordinate. The output of grompp
> > states what the restraint distance is in all cases, based on the coordinates and
> > dimensions chosen for the restraint.
> >
> > -Justin
> >
> > > Thanks again for your help!
> > >
> > >
> > >
> > >
> > > MDP FILE USED:
> > > title = Umbrella pulling simulation
> > > define = -DPOSRES_B
> > > 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
> > > Tcoupl = V-rescale
> > > tau_t = 0.1 0.1 0.1
> > > tc-grps = MOL dop WAT_Cl_Na
> > > ref_t = 300 300 300
> > > ; Pressure coupling
> > > Pcoupl = Parrinello-Rahman
> > > Pcoupltype = Semiisotropic
> > > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > > tau-p = 1.0 1.0
> > > compressibility = 4.6E-5 4.6E-5
> > > ref-p = 1.0 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 = MOL
> > > pull_group1 = Na
> > > 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
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > > Date: Thu, 31 May 2012 13:25:26 -0400
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] boundaries in PMF
> > > >
> > > >
> > > >
> > > > On 5/31/12 1:20 PM, Rebeca García Fandiño wrote:
> > > > > Hi,
> > > > > I am trying to calculate a PMF for an ion along a channel. Everything
> went OK,
> > > > > but when I used g_wham I got a profile with strange dimensions for the
> x-axis.
> > > > > What are the boundaries g_wham is using for calculating the units of
> x-axis?
> > > > >
> > > >
> > > > The values are based on the restraint distances along the reaction
> coordinate.
> > > >
> > > > > I have used:
> > > > > g_wham -it tpr-files.dat -if pullf-files.dat -o file_output.xvg -hist
> > > > > file_histo_output.xvg -unit kCal -cycl yes
> > > > >
> > > > > (version 4.0.7)
> > > > >
> > > > > and the units I got in the x-axis are determined by the boundaries:
> > > > >
> > > > > "Determined boundaries to 0.000035 to 2.603290 "
> > > > >
> > > > > Which are these units? nm?
> > > > >
> > > >
> > > > Yes.
> > > >
> > > > > The z coordinate for my ion explores at least 5 nm!!
> > > > >
> > > > > I am a bit confused about that.
> > > > >
> > > >
> > > > The exact output depends on how you set up the umbrella sampling (in the .mdp
> > > > file). The range of values corresponds to whatever the distances are that are
> > > > sampled in the various windows. Perhaps there is a sign issue here? Do you
> > > > have some restraints that are at negative displacement and others at
> positive?
> > > > Did you set up the .mdp files properly to account for this behavior?
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Research Scientist
> > > > 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.
> > Research Scientist
> > 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.
Research Scientist
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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