[gmx-users] large sim box

[Yan Gao]

Hi There,

I want to use a large simulation box. I did a trial with 15 * 15 * 15 nm box
for 100 steps. genbox_d generates 110k water molecules, or 330k atoms.

It looks like that gromacs can run that large number of atoms. I am sure it
will take a long long long time. However if I really want to simulate it, is
there any way that I can increase the speed? (except using a better cpu, or
paralleling it) Thanks.

My second question is that: If I have to use clusters or super computer,
which one is better? and, do I need a particular software/program to
paralleling it? Thanks.

Thank you for your comments and help!
Yan

I put my .mdp below:
integrator               = md
dt                       = 0.002
; duration  2000 ps
nsteps                   = 100
comm_mode         = linear
nstcomm             = 1
; dump config every 300 fs
nstxout                  = 10
nstvout                  = 10
nstfout             = 10
nstcheckpoint            = 100
nstlog                   = 10
nstenergy                = 10
nstxtcout                = 10
xtc-precision            = 1000000
nstlist                  = 1
ns_type                  = grid
pbc                       = xyz
rlist                    = 1.0    ;1.0
coulombtype              = PME
rcoulomb                 = 1.0    ;1.0
fourierspacing         = 0.2    ;0.1
pme_order         = 4
ewald_rtol          = 1e-5
optimize_fft         = yes
vdwtype             = cut-off
rvdw                     = 1.0    ;1.0
tcoupl                   = Nose-Hoover
tc_grps                  = system
tau_t                    = 0.5
ref_t                    = 300.0
Pcoupl                   = no
annealing         = no
gen_vel                  = no
gen_temp                 = 300.0
gen_seed                 = 173529
constraints              = none
;energy_excl              = C_H C_H
constraint_algorithm     =  lincs
unconstrained_start     = no
lincs_order         = 4
lincs_iter         = 1
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