[gmx-users] boundaries in PMF

[Rebeca García Fandiño]

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...?

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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