[gmx-users] GPU performance, regarding

[RAHUL SURESH]

Hi John

Thank you and adding here the mdp settings

title       = Protein-gas molecule interaction MD simulation
; Run parameters
integrator  = md
nsteps      = 200000000
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 5000        ;
nstvout     = 5000  ;
nstenergy   = 5000    ;
nstlog      = 5000      ;
energygrps  = Protein
; Bond parameters
continuation    = yes           ;
constraint_algorithm = lincs
constraints     = all-bonds     ;
lincs_iter      = 1             ;
lincs_order     = 4
; Neighborsearching
cutoff-scheme = Verlet
ns_type     = grid      ;
nstlist     = 20         ; 10 fs
rlist       = 1.4       ;
rcoulomb    = 1.4       ;
rvdw        = 1.4       ;
; Electrostatics
coulombtype     = PME       ;
pme_order       = 4         ;
fourierspacing  = 0.16      ;
; Temperature coupling
tcoupl      = V-rescale                     ;
tc-grps     = Protein_NO2 Water_and_ions ;
tau_t       = 0.1   0.1                     ;
ref_t       = 300   300                     ;
; Pressure coupling
pcoupl      = Parrinello-Rahman             ;
pcoupltype  = isotropic                     ;
tau_p       = 2.0                           ;
ref_p       = 1.0                           ;
compressibility = 4.5e-5
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ;
; Velocity generation
gen_vel     = no

On Thu, Dec 12, 2019 at 6:01 PM John Whittaker <
johnwhittake at zedat.fu-berlin.de> wrote:

> Hi,
>
> > Hi Users.
> >
> > I am simulating a peptide of 40 residues with small molecules using
> oplsaa
> > ff in Gromacs 2018.20 installed in CUDA environment.. The workstation has
> > 16 Cores and 2 1080Ti card On execution of command gmx_mpi mdrun -v
> > -deffnm
> > md for 100ns it shows no usage of gpu card. For the command  gmx_mpi
> mdrun
> > -v -deffnm md -gputasks 01 -nb gpu, the job is terminated with note
> >  " NB interaction on the gpu were required but not supported for these
> > simulation settings. change your settings or do not require using gpus."
>
> You should provide the content of your .mdp file. According to the error
> message, some of your settings are not compatible with GPU acceleration.
> Without some information about your settings, no one can really help.
>
> - John
>
> >
> > Could anyone explain a solution on this issue?
> >
> > Thank you
> >
> > --
> > *Regards,*
> > *Rahul *
> > --
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-- 
*Regards,*
*Rahul *