Dear:<br><br> 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?<br>
<br>here is my md.mdp:<br><i><br>title = god!<br>cpp = /usr/bin/cpp<br>include = <br>define = <br>integrator = md<br>dt = 0.001<br>
nsteps = 100000000<br>nstxout = 1000000<br>nstvout = 1000000<br>nstlog = 1000000<br>nstenergy = 10000<br>nstxtcout = 100000<br>
xtc_grps =<br>energygrps = Protein POPC SOL ION<br>nstcalcenergy = 1<br>nstlist = 1<br>nstcomm = 1<br>comm_mode = Linear<br>comm-grps = Protein_POPC Water_and_ions<br>
ns_type = grid<br>rlist = 1.2<br>rlistlong = 1.4<br>vdwtype = Switch<br>rvdw = 1.2<br>rvdw_switch = 0.8<br>coulombtype = pme<br>
rcoulomb = 1.2<br>rcoulomb_switch = 0.0<br>fourierspacing = 0.15<br>pme_order = 4<br>DispCorr = no<br>tcoupl = nose-hoover<br>nhchainlength = 1<br>
tc-grps = Protein_POPC Water_and_ions<br>tau_t = 0.5 0.5<br>ref_t = 310 310<br>Pcoupl = parrinello-rahman<br>Pcoupltype = semiisotropic<br>
tau_p = 5.0<br>compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0<br>pbc = xyz<br>gen_vel = no<br>optimize_fft = no<br>constraints = hbonds<br>
constraint_algorithm = Lincs <br></i><br><br><br>Thank you very much<br><br>best<br>