[gmx-users] GPU + surface

[Lucio Montero]

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               =  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
>