[gmx-users] compressing in presence of voids

[Moeed]

Hello,

I am compressing a single extended PE chain (16 nm in length) in a box of
20nm in vacuo to get a more realistic shape of the polymer. Although system
is small (only 362 atoms), whatever -np #  I choose simulation runs very
slowly. Is that because of the presence of voids? Is there a way to speed up
the runs? I have no clue on this. Thanks!

(mpirun -np 4 mdrun_mpi .......    -pd)

starting mdrun 'Polymer'
1000000 steps,   2000.0 ps.
step 0
step 100, will finish Thu Mar 24 19:33:34 2011
step 200, will finish Thu Mar 24 19:29:18 2011
step 300, will finish Thu Mar 24 19:27:42 2011
step 400, will finish Thu Mar 24 19:27:13 2011
step 500, will finish Thu Mar 24 19:27:54 2011



pbc              =  xyz

;        Run control
integrator          =  md
dt                  =  0.002
nsteps              =  1000000 ;5000
nstcomm             =  100

;        Output control
nstenergy           =  100
nstxout             =  100
nstvout             =  0
nstfout             =  0
nstlog              =  1000
nstxtcout          =  1000

;        Neighbor searching
nstlist             =  10
ns_type             =  grid

;        Electrostatics/VdW
coulombtype         =  PME
vdw-type            =  Shift
rcoulomb-switch     =  0
rvdw-switch         =  0.9 ;0

;        Cut-offs
rlist               =  1.25
rcoulomb            =  1.25 ;1.1
rvdw                =  1.0

;        PME parameters
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order          =  4
ewald_rtol          =  1e-5
;optimize_fft      =  yes

;        Temperature coupling
Tcoupl              =  v-rescale
tc-grps             =  System
tau_t               =  0.1
ref_t               =  300

;        Pressure coupling
Pcoupl              =  berendsen;Parrinello-Rahman
Pcoupltype          =  isotropic
tau_p               =  0.5       0.5
compressibility     =  4.5e-5 4.5e-5
ref_p               =  10    10

;        Velocity generation
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

;        Bonds
constraints             = none;all-bonds
constraint-algorithm = lincs
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