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 García Fandiño 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 > > -- > ======================================== > > 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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