Re: [gmx-users] GPU + surface
Hello. ¿Have you removed periodicity?. Because you may only be seeing traversal of water molecules among copies of the periodic system. Lucio Montero Ph. D. student Instituto de Biotecnologia, UNAM Mexico El 08/08/13 07:39, Ondrej Kroutil escribió: 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 = 10 comm_mode= linear nstcomm = 1000 nstxout = 0 nstxtcout= 1000 nstvout = 0 nstfout = 0 nstlog = 1000 xtc_precision= 1 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 -- gmx-users mailing listgmx-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
RE: [gmx-users] GPU + surface
Hi, The -testverlet option is only for testing (as the name implies). Please set the mdp option cutoff-scheme = Verlet Also please update to 4.6.3, as this, potential, issue might have already been resolved. With the Verlet scheme the CPU and GPU should give the same, correct or incorrect, result. Could it be that your system is located partially above and partially below z=0? This will cause problems with ewald-geometry = 3dc. To use this option you need to ensure your whole system is in the same periodic image. Cheers, Berk --- > Date: Thu, 8 Aug 2013 14:39:59 +0200 > From: okrou...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-users] GPU + surface > > 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 = 10 > comm_mode = linear > nstcomm = 1000 > nstxout = 0 > nstxtcout = 1000 > nstvout = 0 > nstfout = 0 > nstlog = 1000 > xtc_precision = 1 > 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 > -- gmx-users mailing listgmx-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
[gmx-users] GPU + surface
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 = 10 comm_mode= linear nstcomm = 1000 nstxout = 0 nstxtcout= 1000 nstvout = 0 nstfout = 0 nstlog = 1000 xtc_precision= 1 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 listgmx-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
