[gmx-users] Tweeking MDP file options to run on GPU

[Szilárd Páll]

Hi,

What is the error you are getting? What is unfortunate about
temperature coupling?

Have you checked out the part of the documentation, especially the
supported features on GPUs part
(http://www.gromacs.org/gpu#Supported_features)?

--
Szilárd



On Mon, Mar 7, 2011 at 3:43 PM, kala <kalabharath at gmail.com> wrote:
> Dear friends
>                 I am trying to run a ternary complex simulation using
> gromacs. so far the simulation is time taking on my dual-core maching
> 36hrs/ns. Fortunately or unfortunately I have a fermi graphics card wherein
> I can run the simulation quite fast. Now the unfortunate thing is the
> temperature coulpling. I am new to gmx and tweeking the mdp files is out of
> my head. I seek for advice for tweeking this mdp file (which i now use for
> cpu calculations)  for fast md using mdrun-gpu.
> My system
> 725 Amino acids
> 2 ligand molecules
> 1 co-ordinate zn Ion
>
> my MDP-file
>
> title       = Protein-ligand complex NVT equilibration
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 500000    ; 2 * 500000 = 1000 ps (1 ns)
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 0         ; suppress .trr output
> nstvout     = 0         ; suppress .trr output
> nstenergy   = 1000      ; save energies every 2 ps
> nstlog      = 1000      ; update log file every 2 ps
> nstxtcout   = 1000      ; write .xtc trajectory every 2 ps
> energygrps  = Protein JZ4
> ; 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
> ns_type     = grid      ; search neighboring grid cells
> nstlist     = 5         ; 10 fs
> rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9       ; 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 is on
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein_JZ4 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 is off
> 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     = yes       ; assign velocities from Maxwell distribution
> gen_temp    = 300       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
> thanks and regards
>
> bharath
>
> --
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