Dear GMX users. I have done simulation of ions and water near quartz surface (ClayFF) using GPU (GTX580) and Gromacs (4.6.1, single precision, 64 bit, SSE4.1, fftw-3.3.3) and have observed strange behavior of water and ions. Its NVT simulation with freezed surface atoms (see .mdp below) and negative charge on surface (deprotonated silanols), system is overall neutral. I used same mdp for normal CPU simulation and GPU simulation, and just added -testverlet option for GPU simulation. In CPU simulation ions and water behaved as expected (see http://i1315.photobucket.com/albums/t587/Andrew_Twister/cpu-simul_zpscf784b46.png) , but in GPU simulation there was a visible flow of ions toward image of lower surface and all water molecules were oriented with hydrogens facing downward and oxygens oriented upwards (see http://i1315.photobucket.com/albums/t587/Andrew_Twister/gpu-simul_zps2c160ea6.png). It looks like there was an applied electric field but it is not. Do you think there is a problem in initial setup of parameters in mdp file? Or maybe problem of freezing groups? With no freeze situation is better, but there is still visible flow and pairing of same ions (see http://i1315.photobucket.com/albums/t587/Andrew_Twister/gpu-no_freeze_zps72ef3938.png). It look as electrostatics problem. Do you have any hints, please? And sorry if I missed similar topic in mailing list, but I couldn't find anything similar.
Ondrej Kroutil integrator = md dt = 0.001 nsteps = 100000 comm_mode = linear nstcomm = 1000 nstxout = 0 nstxtcout = 1000 nstvout = 0 nstfout = 0 nstlog = 1000 xtc_precision = 10000 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 constraints = hbonds constraint_algorithm = lincs lincs_iter = 1 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3dc optimize_fft = yes ; Nose-Hoover temperature coupling Tcoupl = nose-hoover tau_t = 1 tc_grps = system ref_t = 298.15 ; No Pressure ; Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 compressibility = 0 4.6e-5 ref_p = 0 1.0 ; OTHER periodic_molecules = no pbc = xyz ;energygrps = SOL SOH freezegrps = BULK freezedim = Y Y Y gen_vel = yes gen_temp = 298.15 gen_seed = -1 -- Ondřej Kroutil ,, Faculty of Health and Social Studies ----"))' University of South Bohemia OOO Jirovcova 24, Ceske Budejovice OOO The Czech Republic | OO E-mail: okrou...@gmail.com >------ O Mobile: +420 736 537 190 -- 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