I'm studying shear flow, so I exspect the two slabs to be pulled in opposite x direction with the pull speed given. Looking at pull.xvg the slabs are pulled apart with about 1.5nm/ps until the box end (in x) is reached, then they jump back due to pbc. So this is what I would exspect, exept that the speed is much too high.
hm..looking at the com speed vs time as per "g_traj -com -ov -n" for the first diamond slab only, the speed keeps increasing (see attached screenshot). Have I enabled a non constant pull rate somehow?? Alex Berk Hess schrieb: > Hi, > > Yes, speed is in nm/ps. > g_traj -com -ov -n will give the the speed of the slabs as a function > of time. > > If the speed is really 1.2 nm/ps, they should have moved 6 nm in 5 ns, > which is probably not the case, right? > > Could it be that you have pbc issues? > The distance between the two slabs could be taken within the box > or over the boundaries. > Have a look at pullx.xvg to see if it does what you expect. > (the time derivative of pullx.xvg should also give the speed > difference of the slabs). > > Berk > > > Date: Wed, 2 Sep 2009 11:39:22 +0200 > > From: alexander.h...@mytum.de > > To: gmx-users@gromacs.org > > Subject: [gmx-users] t_trxframe speed units > > > > Hey, > > > > 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. > > I calc the avrg speed for a production run of 5ns after 0.5ns equilib. > > 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). > > > > t_trxframe::v contains the speed in [nm/ps] right? > > > > Could someone please comment on this? Why are the diamonds considerably > > faster then the pull speed pull_rate1?? > > This is gromacs4.0.5 by the way. > > Thx, > > Alex > > > > using still this setup: > > > > Here is the pull setup: > > pull = umbrella > > pull_geometry = direction > > pull_ngroups = 1 > > pull_group0 = DIAM > > pull_group1 = DIAM2 > > pulldim = Y Y Y > > pull_k1 = 1000.0 > > pull_rate1 = 0.01 > > pull_vec1 = -1.0 0.0 0.0 > > > > and following geometry: > > > > box_z_max > > water_slab > > diam1 > > water_slab > > diam2 > > box_z_min > > > > rest of the mdp: > > title = 2 diamond surfaces > > cpp = /usr/bin/cpp > > integrator = md > > nsteps = 2500000 > > nstlist = 50 > > nstxout = 50 > > nstvout = 50 > > nstxtcout = 0 > > nstlog = 1000 > > dt = 0.002 > > constraints = h-bonds > > nstenergy = 100 > > ns_type = grid > > coulombtype = pme > > fourierspacing = 0.12 > > pme_order = 4 > > rlist = 0.8 > > rvdw = 0.8 > > rcoulomb = 0.8 > > tcoupl = berendsen > > tc_grps = DIAM DIAMCNST DIAM2 DIAMCNST2 SOL > > energygrps = DIAM DIAMCNST DIAM2 DIAMCNST2 SOL > > tau_t = 0.4 0.4 0.4 0.4 0.4 > > ref_t = 300 300 300 300 300 > > compressibility = 0.0 4.5E-5 > > tau_p = 1.0 1.0 > > ref_p = 1.0 1.0 > > Pcoupl = berendsen > > Pcoupltype = semiisotropic > > gen_vel = no > > > > > > > > > > _______________________________________________ > > 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/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/mailing_lists/users.php > > ------------------------------------------------------------------------ > See all the ways you can stay connected to friends and family > <http://www.microsoft.com/windows/windowslive/default.aspx> > ------------------------------------------------------------------------ > > _______________________________________________ > 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/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/mailing_lists/users.php
<<inline: veloc_2.jpg>>
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