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: jalem...@vt.edu
> To: gmx-users@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
========================================
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