[gmx-users] preparing input file for GPU

[Mark Abraham]

Hi,

You just need to not choose such groups. See
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#output-control

Mark

On Tue, Nov 27, 2018 at 7:10 AM Seketoulie Keretsu <sekekeretsu at gmail.com>
wrote:

> 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
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> Thanking you in anticipation.
>
> Seke
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