[gmx-users] boundaries in PMF

[Justin A. Lemkul]

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

========================================