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

[Hsin-Lin Chiang]

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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