[gmx-users] increasing cut-off and PME grid spacing

[Hsin-Lin Chiang]

Sorry for the confusing symbol.

I tried to change it in this new mail.

Hi,

I want to run mdrun -nt 12 on our cluster.

When I execute,
grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx

I got the message,

Estimate for the relative computational load of the PME mesh part: 1.00

NOTE 1 [file test.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing

Then I changed my mdp to get

Estimate for the relative computational load of the PME mesh part: 0.20

Belos is my new mdp file
I change rlist, rcoulumb, and rvdw from 1 to 12 and fourierspacing from 0.2 to 2 to get the lower relative computational load.
I'm afraid these extreme high value caused some bad effect.

title = ttt
cpp = /lib/cpp
constraints = hbonds
;define = -DFLEX_SPC
integrator = md
emtol = 100.0
emstep = 0.005
dt = 0.002 ; ps !
nsteps = 25000000 ; total 50 ns
nstcomm = 5000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstenergy = 5000
nstlist = 10
ns_type = grid
rlist = 12
rcoulomb = 12
rvdw = 12
coulombtype = PME
fourierspacing = 2
pme_order = 6
optimize_fft = yes
Tcoupl = v-rescale
tc-grps = Protein Non-Protein
;tau_t = 0.1 0.1
tau_t = 0.2 0.2
ref_t = 300 300
energygrps = A-chain B-chain SOL NA
Pcoupl = berendsen
Pcoupltype = isotropic
;tau_p = 0.1
tau_p = 0.25
compressibility = 5.4e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529

Sincerely yours,
Hsin-Lin 
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