[gmx-users] Re: boundaries in PMF

Thu May 31 21:37:15 CEST 2012

Hi,
the center of mass of my channel is at the middle of the ion channel, and it is a symmetric system, so I suppose these results would be OK. Anyway, I will check the options you propose.
Thanks a lot for all your comments!!
Best wishes,
Rebeca.

> Date: Thu, 31 May 2012 20:08:26 +0200
> From: schlesi at uni-mainz.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: boundaries in PMF
> 
> Where is the center of mass of reference group (MOL) located?
> 
> It seems that the COM is near the middle of the ion channel. Since you 
> use 'pull_geometry=distance', g_wham will look only for the distance 
> between 'MOL' and 'Na' and that leads to problem.
> If the com of 'MOL' sits in the center of the channel (which is around 
> 5nm long), one has 2.5nm in both directions. Since g_wham uses only the 
> distance you get the PMF for half of the channel, but with the data of 
> both parts.
> If the channel would be symmetric and the com of 'MOL' would lie exactly 
> in the middle of the channel, this could be ok. But if even one of both 
> assumptions is wrong, the results would be errorous.
> 
> A better approach would be to use 'pull_geometry=direction', since the 
> you define a vector along which the windows lie and do not have the 
> problem that the distance is in both directions (along positive and 
> negative vector) the same.
> Only problem could be that g_wham supports 'pull_geometry=direction' 
> only from gromacs 4.5.x (don't know this, since instead of umbrella 
> smapling i use thermodynamik integration, where one uses constraints 
> (instead of restraints) and integrates the constraint-force; but the 
> conceptual problem with 'distance/direction' is the same).
> 
> Another approach (with 'pull_geometry=distance') would be to use a 
> reference group which is just outside of the channel (like going some 
> steps away from the channel, along the vector which goes through the 
> channel). If there is only water, it would be bad, because then the 
> reference group would be move away.
> But then on could use the entry and exit of the channel as a reference 
> point for two simulations. In the case that the entry is the reference 
> group, the PMF would be ill defined near the entry, but from the 
> simulation with the exit as reference you would get the right PMF for 
> the entry region and vice versa.
> 
> Greetings
> Thomas
> 
> 
> Am 31.05.2012 19:39, schrieb gmx-users-request at gromacs.org:
> > 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 Garc?a Fandi?o 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
> 
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