[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

[Albert]

Dear:

  I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that the
efficiency for such simulation is only 3ns/day..... I am wondering what
happen to my system or gromacs? What can I do to fasten the simulation?

here is my md.mdp:
*
title                    = god!
cpp                      = /usr/bin/cpp
include                  =
define                   =
integrator               = md
dt                       = 0.001
nsteps                   = 100000000
nstxout                  = 1000000
nstvout                  = 1000000
nstlog                   = 1000000
nstenergy                = 10000
nstxtcout                = 100000
xtc_grps                 =
energygrps         = Protein POPC SOL ION
nstcalcenergy            = 1
nstlist                  = 1
nstcomm                  = 1
comm_mode                = Linear
comm-grps                = Protein_POPC    Water_and_ions
ns_type                  = grid
rlist                    = 1.2
rlistlong         = 1.4
vdwtype             = Switch
rvdw                     = 1.2
rvdw_switch         = 0.8
coulombtype              = pme
rcoulomb                 = 1.2
rcoulomb_switch         = 0.0
fourierspacing         = 0.15
pme_order         = 4
DispCorr             = no
tcoupl                   = nose-hoover
nhchainlength            = 1
tc-grps                  = Protein_POPC    Water_and_ions
tau_t                    = 0.5            0.5
ref_t                    = 310         310
Pcoupl                   = parrinello-rahman
Pcoupltype               = semiisotropic
tau_p                    = 5.0
compressibility          = 4.5e-5       4.5e-5
ref_p                    = 1.0          1.0
pbc             = xyz
gen_vel                  = no
optimize_fft         = no
constraints              = hbonds
constraint_algorithm     = Lincs
*


Thank you very much

best
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