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OK,<br>however, just one point about your last comment:<br><br>> I suspect this is why g_wham is finding a range of values only equal to half of <br>> your expected reaction coordinate; it is considering only the positive <br>> displacement along the reaction coordinate.<br><br>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.<br><br>Rebeca.<br><br><div><div id="SkyDrivePlaceholder"></div>> Date: Thu, 31 May 2012 15:42:06 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Re: boundaries in PMF<br>> <br>> <br>> <br>> On 5/31/12 3:37 PM, Rebeca García Fandiño wrote:<br>> > Hi,<br>> > the center of mass of my channel is at the middle of the ion channel, and it is<br>> > a symmetric system, so I suppose these results would be OK. Anyway, I will check<br>> > the options you propose.<br>> <br>> If you are sampling regions above and below the channel/membrane, then the <br>> "distance" geometry is not appropriate; you need either "direction" or (perhaps <br>> the most flexible option) "position." There are a number of useful discussions <br>> on such topics in the list archive and in my umbrella sampling tutorial for you <br>> to consider. You can likely create a series of .tpr files from new .mdp files <br>> with correct options to run the analysis.<br>> <br>> I suspect this is why g_wham is finding a range of values only equal to half of <br>> your expected reaction coordinate; it is considering only the positive <br>> displacement along the reaction coordinate.<br>> <br>> -Justin<br>> <br>> > Thanks a lot for all your comments!!<br>> > Best wishes,<br>> > Rebeca.<br>> ><br>> > > Date: Thu, 31 May 2012 20:08:26 +0200<br>> > > From: schlesi@uni-mainz.de<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: [gmx-users] Re: boundaries in PMF<br>> > ><br>> > > Where is the center of mass of reference group (MOL) located?<br>> > ><br>> > > It seems that the COM is near the middle of the ion channel. Since you<br>> > > use 'pull_geometry=distance', g_wham will look only for the distance<br>> > > between 'MOL' and 'Na' and that leads to problem.<br>> > > If the com of 'MOL' sits in the center of the channel (which is around<br>> > > 5nm long), one has 2.5nm in both directions. Since g_wham uses only the<br>> > > distance you get the PMF for half of the channel, but with the data of<br>> > > both parts.<br>> > > If the channel would be symmetric and the com of 'MOL' would lie exactly<br>> > > in the middle of the channel, this could be ok. But if even one of both<br>> > > assumptions is wrong, the results would be errorous.<br>> > ><br>> > > A better approach would be to use 'pull_geometry=direction', since the<br>> > > you define a vector along which the windows lie and do not have the<br>> > > problem that the distance is in both directions (along positive and<br>> > > negative vector) the same.<br>> > > Only problem could be that g_wham supports 'pull_geometry=direction'<br>> > > only from gromacs 4.5.x (don't know this, since instead of umbrella<br>> > > smapling i use thermodynamik integration, where one uses constraints<br>> > > (instead of restraints) and integrates the constraint-force; but the<br>> > > conceptual problem with 'distance/direction' is the same).<br>> > ><br>> > > Another approach (with 'pull_geometry=distance') would be to use a<br>> > > reference group which is just outside of the channel (like going some<br>> > > steps away from the channel, along the vector which goes through the<br>> > > channel). If there is only water, it would be bad, because then the<br>> > > reference group would be move away.<br>> > > But then on could use the entry and exit of the channel as a reference<br>> > > point for two simulations. In the case that the entry is the reference<br>> > > group, the PMF would be ill defined near the entry, but from the<br>> > > simulation with the exit as reference you would get the right PMF for<br>> > > the entry region and vice versa.<br>> > ><br>> > > Greetings<br>> > > Thomas<br>> > ><br>> > ><br>> > > Am 31.05.2012 19:39, schrieb gmx-users-request@gromacs.org:<br>> > > > Thanks a lot for your quick answer. The mdp file I have used is copied<br>> > > > below. What is strange is that when I look at the *gro files for the<br>> > > > different windows (100 windows in total), i. e: window 1: 8704Na Na56458<br>> > > > 5.134 5.085 5.824 window 50: 8704Na Na56458 5.053 5.081 3.459 window<br>> > > > 100: 8704Na Na56458 4.990 5.042 0.951 you can see that the z-coordinate<br>> > > > goes from 0.951 to 5.824 nm I should have a total distance in the x-axis<br>> > > > of about 5 nm, and however, the boundaries calculated by g_wham are<br>> > > > "Determined boundaries to 0.000035 to 2.603290 " Can you see anything in<br>> > > > the mdp file which is causing this behaviour...? Thanks again for your<br>> > > > help! MDP FILE USED: title = Umbrella pulling simulation define =<br>> > > > -DPOSRES_B define = ; Run parameters integrator = md dt = 0.002 tinit =<br>> > > > 0 nsteps = 500000 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 5000<br>> > > > ; every 10 ps nstvout = 5000 nstfout = 5000 nstxtcout = 5000 ; every 10<br>> > > > ps nstenergy = 5000 ; Bond parameters constraint_algorithm = lincs<br>> > > > constraints = all-bonds continuation = yes ; Single-range cutoff scheme<br>> > > > nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME<br>> > > > electrostatics parameters coulombtype = PME fourierspacing = 0.12<br>> > > > fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol =<br>> > > > 1e-5 optimize_fft = yes ;Berendsen temperature coupling is on Tcoupl =<br>> > > > V-rescale tau_t = 0.1 0.1 0.1 tc-grps = MOL dop WAT_Cl_Na ref_t = 300<br>> > > > 300 300 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype =<br>> > > > Semiisotropic ; Time constant (ps), compressibility (1/bar) and<br>> > > > reference P (bar) tau-p = 1.0 1.0 compressibility = 4.6E-5 4.6E-5 ref-p<br>> > > > = 1.0 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary<br>> > > > conditions are on in all directions pbc = xyz ; Long-range dispersion<br>> > > > correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry<br>> > > > = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1<br>> > > > pull_group0 = MOL pull_group1 = Na pull_init1 = 0 pull_rate1 = 0.0<br>> > > > pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps<br>> > > > pull_nstfout = 1000 ; every 2 ps<br>> > > >> > Date: Thu, 31 May 2012 13:25:26 -0400<br>> > > >> > From:jalemkul@vt.edu<br>> > > >> > To:gmx-users@gromacs.org<br>> > > >> > Subject: Re: [gmx-users] boundaries in PMF<br>> > > >> ><br>> > > >> ><br>> > > >> ><br>> > > >> > On 5/31/12 1:20 PM, Rebeca Garc?a Fandi?o wrote:<br>> > > >>> > > Hi,<br>> > > >>> > > I am trying to calculate a PMF for an ion along a channel. Everything<br>> > went OK,<br>> > > >>> > > but when I used g_wham I got a profile with strange dimensions for<br>> > the x-axis.<br>> > > >>> > > What are the boundaries g_wham is using for calculating the units of<br>> > x-axis?<br>> > > >>> > ><br>> > > >> ><br>> > > >> > The values are based on the restraint distances along the reaction<br>> > coordinate.<br>> > > >> ><br>> > > >>> > > I have used:<br>> > > >>> > > g_wham -it tpr-files.dat -if pullf-files.dat -o file_output.xvg -hist<br>> > > >>> > > file_histo_output.xvg -unit kCal -cycl yes<br>> > > >>> > ><br>> > > >>> > > (version 4.0.7)<br>> > > >>> > ><br>> > > >>> > > and the units I got in the x-axis are determined by the boundaries:<br>> > > >>> > ><br>> > > >>> > > "Determined boundaries to 0.000035 to 2.603290"<br>> > > >>> > ><br>> > > >>> > > Which are these units? nm?<br>> > > >>> > ><br>> > > >> ><br>> > > >> > Yes.<br>> > > >> ><br>> > > >>> > > The z coordinate for my ion explores at least 5 nm!!<br>> > > >>> > ><br>> > > >>> > > I am a bit confused about that.<br>> > > >>> > ><br>> > > >> ><br>> > > >> > The exact output depends on how you set up the umbrella sampling (in the<br>> > .mdp<br>> > > >> > file). The range of values corresponds to whatever the distances are<br>> > that are<br>> > > >> > sampled in the various windows. Perhaps there is a sign issue here? Do you<br>> > > >> > have some restraints that are at negative displacement and others at<br>> > positive?<br>> > > >> > Did you set up the .mdp files properly to account for this behavior?<br>> > > >> ><br>> > > >> > -Justin<br>> > ><br>> > > --<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at<br>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> ><br>> ><br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul, Ph.D.<br>> Research Scientist<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div> </div></body>
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