[gmx-users] why it is so slow

[Justin Lemkul]

On 11/1/12 12:55 PM, Albert wrote:
> hello:
>
>   I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for
> 16 different temperature with exchange step 300.
>

Based on your .mdp file, you're not doing NPT (pcoupl = no).

> mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s remd_.tpr
> -multi 16 -replex 300
>
>
> I found that it will require 1 months to be finished which is a really long time.
>
> I am just wondering is there anything I did wrong for the .mdp so that it is so
> slow? here is my .mdp file.
>

One month is not very long, especially if you are running on CPU and not GPU. 
How many atoms are in your system?  How did you decide that 24 CPU per replica 
was appropriate?  How did you decide on your exchange frequency?  Exchanging 
every 0.6 ps sounds awfully frequent, but I'm no REMD expert so I'll leave that 
for others to comment on.

-Justin

> thank you very much
>
>
>
>
>
> title = Protein-ligand complex NPT equilibration
> ; Run parameters
> integrator = sd ;
> nsteps = 20000000 ; 2 * 50000 = 100 ps
> dt = 0.002 ; 2 fs
> nstxout = 0 ; save coordinates every 0.2 ps
> nstvout = 0 ; save velocities every 0.2 ps
> nstfout = 0
>
> nstxtcout = 500
> nstenergy = 100 ; save energies every 0.2 ps
> nstlog = 1000 ; update log file every 0.2 ps
> energygrps = Protein_LIG
> ; 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 = simple ; search neighboring grid cells
> nstlist = 0 ; 10 fs
> rlist = 0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
> rvdw = 0 ; short-range van der Waals cutoff (in nm)
>
> ; Electrostatics
> coulombtype = cutoff ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.15 ; grid spacing for FFT
>
> ; Temperature coupling
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein_LIG  ; two coupling groups - more accurate
> tau_t = 0.1 ; time constant, in ps
> ref_t = 310 ; reference temperature, one for each group, in K
>
> ; Pressure coupling
> pcoupl = no    ; pressure coupling is on for NPT
> ; Periodic boundary conditions
> ; Pressure coupling
> pcoupl = no    ; pressure coupling is on for NPT
> ; Periodic boundary conditions
> tau_p       = 2.0                           ; time constant, in ps
> ref_p       = 1.0                           ; reference pressure, in bar
> pbc=no
> ; Dispersion correction
> DispCorr = no ; account for cut-off vdW scheme
> pcoupltype  = isotropic                     ; uniform scaling of box vectors
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 310 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
> ld_seed=-1
>
> ; IMPLICIT SOLVENT ALGORITHM
> implicit_solvent = GBSA
> comm_mode = ANGULAR
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = OBC
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 0
> ; Dielectric coefficient of the implicit solvent
> gb_epsilon_solvent = 80
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> gb_dielectric_offset = 0.009
> sa_algorithm = Ace-approximation
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
> ; The value -1 will set default value for Still/HCT/OBC GB-models.
> sa_surface_tension = 2.25936
>
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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