[gmx-users] GPU + surface
gmx3 at hotmail.com
Thu Aug 8 15:45:08 CEST 2013
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.
> Date: Thu, 8 Aug 2013 14:39:59 +0200
> From: okroutil at gmail.com
> To: gmx-users at 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
> , 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
> 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
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