<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style></head>
<body class='hmmessage'><div dir='ltr'>
Thanks a lot for your quick answer.<br>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:<br><br>window 1: 8704Na Na56458 5.134 5.085 5.824<br>window 50: 8704Na Na56458 5.053 5.081 3.459<br>window 100: 8704Na Na56458 4.990 5.042 0.951<br><br>you can see that the z-coordinate goes from 0.951 to 5.824 nm <br><br>I should have a total distance in the x-axis of about 5 nm, and however, the boundaries calculated by g_wham are<br><br> "Determined boundaries to 0.000035 to 2.603290 "<br><br>Can you see anything in the mdp file which is causing this behaviour...?<br><br>Thanks again for your help!<br><br><br><br><br>MDP FILE USED:<br>title = Umbrella pulling simulation<br>define = -DPOSRES_B<br>define =<br>; Run parameters<br>integrator = md<br>dt = 0.002<br>tinit = 0<br>nsteps = 500000 ; 1 ns<br>nstcomm = 10<br>; Output parameters<br>nstxout = 5000 ; every 10 ps<br>nstvout = 5000<br>nstfout = 5000<br>nstxtcout = 5000 ; every 10 ps<br>nstenergy = 5000<br>; Bond parameters<br>constraint_algorithm = lincs<br>constraints = all-bonds<br>continuation = yes<br>; Single-range cutoff scheme<br>nstlist = 5<br>ns_type = grid<br>rlist = 1.4<br>rcoulomb = 1.4<br>rvdw = 1.4<br>; PME electrostatics parameters<br>coulombtype = PME<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;Berendsen temperature coupling is on<br>Tcoupl = V-rescale<br>tau_t = 0.1 0.1 0.1<br>tc-grps = MOL dop WAT_Cl_Na<br>ref_t = 300 300 300<br>; Pressure coupling<br>Pcoupl = Parrinello-Rahman<br>Pcoupltype = Semiisotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>tau-p = 1.0 1.0<br>compressibility = 4.6E-5 4.6E-5<br>ref-p = 1.0 1.0<br>; Generate velocities is off<br>gen_vel = no<br>; Periodic boundary conditions are on in all directions<br>pbc = xyz<br>; Long-range dispersion correction<br>DispCorr = EnerPres<br>; Pull code<br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = N N Y<br>pull_start = yes<br>pull_ngroups = 1<br>pull_group0 = MOL<br>pull_group1 = Na<br>pull_init1 = 0<br>pull_rate1 = 0.0<br>pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>pull_nstxout = 1000 ; every 2 ps<br>pull_nstfout = 1000 ; every 2 ps<br><br><br><br><br><br><br><br><br><br><div><div id="SkyDrivePlaceholder"></div>> 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 García Fandiño wrote:<br>> > Hi,<br>> > I am trying to calculate a PMF for an ion along a channel. Everything went OK,<br>> > but when I used g_wham I got a profile with strange dimensions for the x-axis.<br>> > What are the boundaries g_wham is using for calculating the units of x-axis?<br>> ><br>> <br>> The values are based on the restraint distances along the reaction 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 .mdp <br>> file). The range of values corresponds to whatever the distances are 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 positive? <br>> Did you set up the .mdp files properly to account for this behavior?<br>> <br>> -Justin<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>
</html>