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Hi,<br><br>Yes, speed is in nm/ps.<br>g_traj -com -ov -n will give the the speed of the slabs as a function of time.<br><br>If the speed is really 1.2 nm/ps, they should have moved 6 nm in 5 ns,<br>which is probably not the case, right?<br><br>Could it be that you have pbc issues?<br>The distance between the two slabs could be taken within the box<br>or over the boundaries.<br>Have a look at pullx.xvg to see if it does what you expect.<br>(the time derivative of pullx.xvg should also give the speed difference of the slabs).<br><br>Berk<br><br>> Date: Wed, 2 Sep 2009 11:39:22 +0200<br>> From: alexander.herz@mytum.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] t_trxframe speed units<br>> <br>> Hey,<br>> <br>> I averaged the speed of the diamond slabs, so I wrote a small gmx tools which averages t_trxframe.v[i] where i iterates over the diam atoms.<br>> I calc the avrg speed for a production run of 5ns after 0.5ns equilib.<br>> I get an avrg speed of 1.2 [nm/ps], so this is not just some fluctuation (last time I only looked at the last frame output by gromacs).<br>> <br>> t_trxframe::v contains the speed in [nm/ps] right?<br>> <br>> Could someone please comment on this? Why are the diamonds considerably<br>> faster then the pull speed pull_rate1??<br>> This is gromacs4.0.5 by the way.<br>> Thx,<br>> Alex<br>> <br>> using still this setup:<br>> <br>> Here is the pull setup:<br>> pull = umbrella<br>> pull_geometry = direction<br>> pull_ngroups = 1<br>> pull_group0 = DIAM<br>> pull_group1 = DIAM2<br>> pulldim = Y Y Y<br>> pull_k1 = 1000.0<br>> pull_rate1 = 0.01<br>> pull_vec1 = -1.0 0.0 0.0<br>> <br>> and following geometry:<br>> <br>> box_z_max<br>> water_slab<br>> diam1<br>> water_slab<br>> diam2<br>> box_z_min<br>> <br>> rest of the mdp:<br>> title = 2 diamond surfaces<br>> cpp = /usr/bin/cpp<br>> integrator = md<br>> nsteps = 2500000<br>> nstlist = 50<br>> nstxout = 50<br>> nstvout = 50<br>> nstxtcout = 0<br>> nstlog = 1000<br>> dt = 0.002<br>> constraints = h-bonds<br>> nstenergy = 100<br>> ns_type = grid<br>> coulombtype = pme<br>> fourierspacing = 0.12<br>> pme_order = 4<br>> rlist = 0.8<br>> rvdw = 0.8<br>> rcoulomb = 0.8<br>> tcoupl = berendsen<br>> tc_grps = DIAM DIAMCNST DIAM2 DIAMCNST2 SOL<br>> energygrps = DIAM DIAMCNST DIAM2 DIAMCNST2 SOL<br>> tau_t = 0.4 0.4 0.4 0.4 0.4<br>> ref_t = 300 300 300 300 300<br>> compressibility = 0.0 4.5E-5<br>> tau_p = 1.0 1.0<br>> ref_p = 1.0 1.0<br>> Pcoupl = berendsen<br>> Pcoupltype = semiisotropic<br>> gen_vel = no<br>> <br>> <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/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/mailing_lists/users.php<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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