[gmx-users] preparing input file for GPU

[Seketoulie Keretsu]

I am running a protein ligand simulation for the first time after
installation of GPU. When i execute mdrun i got this message,
"Multiple energy groups is not implemented for GPUs, falling back to
the CPU. ". I understand i have to remove the energy group in the .mdp
file. But I am not sure how to do that. What are the changes i should
do to make it compatible for GPU execution? Kindly suggest me a
material or link where i can find the information. I have looked at
some gromacs manual but could not really find for the specific
problem. Suggestions on where to look will be appreciated too.

Here is my .mdp file:
title       = Protein-ligand complex MD simulation
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 100000    ; 2 * 100000 = 200 ps (0.2 ns)
dt          = 0.002     ; 2 fs
; Output control
nstxout             = 0         ; suppress .trr output
nstvout             = 0         ; suppress .trr output
nstenergy           = 5000      ; save energies every 10.0 ps
nstlog              = 5000      ; update log file every 10.0 ps
nstxout-compressed  = 5000      ; write .xtc trajectory every 10.0 ps
compressed-x-grps   = System
energygrps          = Protein UNK
; Bond parameters
continuation    = yes           ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type         = grid      ; search neighboring grid cells
nstlist         = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb        = 1.4       ; short-range electrostatic cutoff (in nm)
rvdw            = 1.4       ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein_UNK  Water_and_ions    ; two coupling groups -
more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature,
one for each group, in K
; Pressure coupling
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal
compressibility of water, bar^-1
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no        ; assign velocities from Maxwell distribution
xxxxxxxxxxxxxxxxxxxxxxxxxxxxx       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxx       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Thanking you in anticipation.

Seke