>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
Thank you for reply The original .mdp is below and the number of atoms is 20171 The difference is only in rlist, rcoulomb, rvdw, and fourierspacing 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 = 1 rcoulomb = 1 rvdw = 1 coulombtype = PME fourierspacing = 0.2 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 Hsin-Lin
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