[gmx-users] simulations in vacuum in parallel

[Justin A. Lemkul]

Qinghua Liao wrote:
> Dear gmx users,
> 
> I tried to do simulations of a small peptide in vacuum, I found that it 
> failed to be run in parallel, even when I use only 8 cores.
> My system only have hundreds of atoms. the problem may be resulted from 
> domain decomposition. When I choose particle
> decomposition method, for small system, I can use 4 threads but not 8, 
> and for a little bigger systems, I can only use 8 threads.
> 
> For this situation, is it normal? Is there some solution to this 
> problem? Thanks very much!

You can't necessarily parallelize any system over an arbitrary number of 
processors.  Even if you could, you'd likely lose performance due to the latency 
of node-node communication.  For a system of a few hundred atoms, running in 
parallel may not even yield significantly better performance over a serial run.

-Justin

> 
> The following lines are my mdp file for the vacuum simulation:
> 
>  title               =  PDXN  of Abeta in H2O
> ;cpp                 =  /lib/cpp   ; prepocessor of the current machine
> define              = ;-DPOSRES 
> integrator          =  md       ; molecular dynamics algorithm
> tinit               =  0.0      ; start time and timestep in ps
> dt                  =  0.002    ; time step in ps
> nsteps              =  500000000   ; number of steps for 1000ns run
> emtol               =  100    ; convergence criterion
> emstep              =  0.05      ; intial step size
> nstlist             =  10       ; step frequency for updating neighbour list
> ns_type             =  grid ;simple     ; method for neighbour searching (?)
> nstxout             =  5000    ; frequency for writing coords to output 
> .trr file
> nstvout             =  0     ; frequency for writing velocities to 
> output...should be same as nstxout
> nstfout             =  0        ; frequency for writing forces to output
> nstlog              =  5000      ; frequency for writing energies to log 
> file
> nstenergy           =  5000      ; frequency for writing energies to 
> energy file
> nstxtcout           =  5000     ; frequency for writing coords to xtc traj
> xtc_grps            =  system   ; group(s) whose coords are to be 
> written in xtc traj
> energygrps          =  system   ; group(s) whose energy is to be written 
> in energy file
> pbc                 =  no      ; use pbc
> rlist               =  0      ; cutoff lengths (nm)
> epsilon_r           =  1.0      ; Dielectric constant (DC) for 
> twin-range or DC of reaction field
> niter               =  100      ; Some thingies for future use 
> fourierspacing    =  0.16
> fourier_nx          =  30
> fourier_ny          =  30
> fourier_nz          =  30
> coulombtype         =  Cut-off      ; truncation for minimisation, with 
> large cutoff
> rcoulomb            =  0
> rcoulomb-switch     =  0
> vdw-type                 = Cut-off  ; truncation for minimisation, with 
> large cutoff
> rvdw-switch              = 0
> rvdw                     = 0   ; cut-off lengths
> ;pme_order                = 6    ; EWALD/PME/PPPM parameters
> ;ewald_rtol               = 1e-05
> ;ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = yes
>  Free energy control stuff
> free_energy              = yes
> init_lambda              = 0.0
> delta_lambda             = 0
> sc_alpha                 =0.5
> sc-power                 =1.0
> sc-sigma                 = 0.3
> comm_mode           = angular
> nstcomm             =  10        ; number of steps for centre of mass 
> motion removal (in vacuo only!)
> Tcoupl              =  V-rescale
> tc_grps             = system ; MVN_Protein ;SOL_Ion ; Non-Protein 
> tau_t               = 0.01 
> ref_t               = 300
> Pcoupl              = no ; Parrinello-Rahman ; Pressure coupling    
> ;Pcoupltype          =  Isotropic
> ;tau_p               =  1.0  1.0 1.0
> ;ref_p               =  1.0  1.0 1.0
> ;compressibility     =  4.5e-5   ; compressibility
> ;
> annealing           =  no       ; SIMULATED ANNEALING CONTROL 
> ;zero_temp_time      =  0        ; Time at which temperature should be 
> zero (ps)
> gen_vel             =  yes
> gen_temp            =  300
> gen_seed            =  -1
> constraints         =  all-bonds  ; OPTIONS FOR BOND CONSTRAINTS 
> constraint-algorithm  = Lincs   ; Type of constraint algorithm
> lincs_order         =  4        ; Highest order in the expansion of the 
> constraint coupling matrix
> lincs_iter          =  1
> lincs_warnangle     =  30       ; Lincs will write a warning to the 
> stderr if in one step a bond rotates 
>                                ; over more degrees than 
> unconstrained-start      = no   ; Do not constrain the start configuration
> ;Shake-SOR                = no   ; Use successive overrelaxation to 
> reduce the number of shake iterations
> ;shake-tol                = 1e-04 ; Relative tolerance of shake
> morse                    = no   ; Convert harmonic bonds to morse potentials
> 
> 
> -- 
> Best Regards,
> 
> Qinghua
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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