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<font size="2"><b></b><font size="2">Hi,
<br /></font></font><font size="2">
<br />I want to run mdrun -nt 12 on our cluster.
<br />
<br />
</font><font size="2">When I execute,
<br />
grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx
<br /></font><font size="2">
<br />I got the message,
<br /></font><font size="2">
<br />Estimate for the relative computational load of the PME mesh part: 1.00
<br />
<br />
NOTE 1 [file test.mdp]:
<br />
  The optimal PME mesh load for parallel simulations is below 0.5
<br />
  and for highly parallel simulations between 0.25 and 0.33,
<br />
  for higher performance, increase the cut-off and the PME grid spacing
<br />
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<br />
<br />Then I changed my mdp to get
<br />
<br />Estimate for the relative computational load of the PME mesh part: 0.20
<br />
<br />Belos is my new mdp file
<br />I change rlist, rcoulumb, and rvdw from 1 to 12 and </font><font size="2">fourierspacing from 0.2 to 2 </font><font size="2">to get the lower </font><font size="2">relative computational load.
<br />I'm afraid these extreme high value caused some bad effect.
<br /></font><font size="2"><font size="2">
<br />title        = ttt
<br />cpp                 =  /lib/cpp
<br />constraints         =  hbonds
<br />;define              =  -DFLEX_SPC
<br />integrator          =  md
<br />emtol               =  100.0
<br />emstep              =  0.005
<br />dt                  =  0.002    ; ps !
<br />nsteps              =  25000000  ; total 50 ns
<br />nstcomm             =  5000
<br />nstxout             =  5000
<br />nstvout             =  5000
<br />nstfout             =  5000
<br />nstlog              =  5000
<br />nstenergy           =  5000
<br />nstlist             =  10
<br />ns_type             =  grid
<br />rlist               =  12
<br />rcoulomb            =  12
<br />rvdw                =  12
<br />coulombtype         =  PME
<br />fourierspacing      =  2
<br />pme_order           =  6
<br />optimize_fft        =  yes
<br />Tcoupl              =  v-rescale
<br />tc-grps             =  Protein Non-Protein
<br />;tau_t               =  0.1  0.1
<br />tau_t               =  0.2 0.2
<br />ref_t               =  300 300
<br />energygrps          =  A-chain B-chain SOL NA
<br />Pcoupl              =  berendsen
<br />Pcoupltype          =  isotropic
<br />;tau_p               =  0.1
<br />tau_p               =  0.25
<br />compressibility     =  5.4e-5
<br />ref_p               =  1.0
<br />gen_vel             =  yes
<br />gen_temp            =  300
<br />gen_seed            =  173529
<br />
<br />
<br />Sincerely yours,
<br />Hsin-Lin</font><span style="font-weight: bold;">
<br /></span>
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