Dear: I am using gromacs for membrane simulation (under CHARMM36 FF) which contains around 80,000 atoms. I've submitted over 200 CPU in the cluster for such system with 2 fs time step. And what really astonished is that the efficiency for such simulation is only 3ns/day..... I am wondering what happen to my system or gromacs? What can I do to fasten the simulation?
here is my md.mdp: * title = god! cpp = /usr/bin/cpp include = define = integrator = md dt = 0.001 nsteps = 100000000 nstxout = 1000000 nstvout = 1000000 nstlog = 1000000 nstenergy = 10000 nstxtcout = 100000 xtc_grps = energygrps = Protein POPC SOL ION nstcalcenergy = 1 nstlist = 1 nstcomm = 1 comm_mode = Linear comm-grps = Protein_POPC Water_and_ions ns_type = grid rlist = 1.2 rlistlong = 1.4 vdwtype = Switch rvdw = 1.2 rvdw_switch = 0.8 coulombtype = pme rcoulomb = 1.2 rcoulomb_switch = 0.0 fourierspacing = 0.15 pme_order = 4 DispCorr = no tcoupl = nose-hoover nhchainlength = 1 tc-grps = Protein_POPC Water_and_ions tau_t = 0.5 0.5 ref_t = 310 310 Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 pbc = xyz gen_vel = no optimize_fft = no constraints = hbonds constraint_algorithm = Lincs * Thank you very much best
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