Hsin-Lin Chiang wrote:
**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.
If the simulation is even stable, it will be horribly inaccurate. 12 nm cutoffs
are unheard of and 2-nm grid spacing is about 20 times too large.
Without seeing the original .mdp file that gave the high PME load, and without a
further description about how large the system is (number of atoms), it is hard
to say what you should do. Some system do not parallelize well, but I imagine
you should be able to get better performance.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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