[gmx-users] GPU + surface

[Ondrej Kroutil]

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:  okroutil at gmail.com
>------    O         Mobile:  +420 736 537 190