[gmx-users] (no subject)

[M.Naser]

Hi All,

I have been running a system consisting 20368 atoms on a single node with
the following parameters. The speed is about 3 days for a nano seconds. I
have been wondering whether this is the expected speed in gromacs. I tried
to run it on 4 nodes and unfortunately did not scale well. It appeared to
be faster on a single node.Am I making any mistake along the line?

And also, is there any tool to count the hydrogen bond between protein and
water molecule?

Thanks in advance,

Abu

integrator          = md
dt                  = 0.001
nsteps              = 2000000
tint		    = 0
init_step           = 0
comm_mode           = No
nstcomm             = 1
nstlist             = 10
ns_type 	    = grid
pbc                 = full
rlist		    = 0.9
coulombtype	    = PME
rcoulomb-switch     = 0
rcoulomb            = 0.9
vdwtype		    = switch;cut-off
rvdw-switch	    = 0.8
rvdw                = 0.9; vdw/lj cutoff in nm
fourierspacing     = 0.12
pme_order          = 4
ewald_rtol          =1e-5
ewald_geometry      =3dc
surface_epsilon     =0
optimize_fft        =yes
DispCorr            = no
table-extension     = 1
Tcoupl              =  Berendsen
tc_grps	            = system
tau_t               =  0.1
ref_t		    =  300
Pcoupl              = no
pcoupltype          = isotropic
tau_p               = 1.0
compressibility     = 4.5e-5
ref_p               = 1.0
gen_vel             =  yes
gen_temp 	    =  300
gen_seed            =  284623
constraints         =  none
nstxout            = 100
nstvout            = 100
nstfout            = 0
nstlog            =  100
nstenergy         =  100
nstxtcout         =  100
xtc_precision     = 1000








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