[gmx-users] simulations in vacuum in parallel

[Qinghua Liao]

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!

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120412/3c3b5251/attachment.html>