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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
