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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