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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