[gmx-users] Re: boundaries in PMF

Rebeca García Fandiño regafan at hotmail.com
Thu May 31 21:51:28 CEST 2012 

OK,
however, just one point about your last comment:

> 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.

It seems like all the channel is explored, not only one half. If g_wham was only considering the positive displacement I should see a profile for just one half of the channel, shouldn´t I? and I can see a profile typical for the entire channel.

Rebeca.

> Date: Thu, 31 May 2012 15:42:06 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: boundaries in PMF
> 
> 
> 
> 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
> 
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