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: jalem...@vt.edu > To: gmx-users@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: schl...@uni-mainz.de > > > To: gmx-users@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-requ...@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:jalem...@vt.edu > > > >> > To:gmx-users@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 > > > > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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