[gmx-users] Re: boundaries in PMF

Thu May 31 21:42:06 CEST 2012

On 5/31/12 3:37 PM, Rebeca García Fandiño wrote:
> 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.

If you are sampling regions above and below the channel/membrane, then the 
"distance" geometry is not appropriate; you need either "direction" or (perhaps 
the most flexible option) "position."  There are a number of useful discussions 
on such topics in the list archive and in my umbrella sampling tutorial for you 
to consider.  You can likely create a series of .tpr files from new .mdp files 
with correct options to run the analysis.

I suspect this is why g_wham is finding a range of values only equal to half of 
your expected reaction coordinate; it is considering only the positive 
displacement along the reaction coordinate.

-Justin

> 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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-- 
========================================

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

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