Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger systems (~ 160000 atoms) using the same gromacs installation on the same hardware, and they run much faster than this (200 ps per 40 cpu hours).
Can anybody suggest why this is happening ? Is it because of latency in the cpu communication? If so, what is the workaround ? My .mdp script is below. These are the run commands. grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o heat.tpr mpirun -np 4 ~/bin/mdrun_mpi -np 4 -v -s heat.tpr -o heat.trr -c heat.gro -e heat -g heat.log > & heat.out ;########################################### ; heat.mdp ; title = heating cpp = /usr/bin/cpp constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes integrator = md nsteps = 25000 dt = 0.002 comm_mode = linear nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid pbc = xyz ; ------------------ coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rlist = 1.0 rvdw = 1.0 fourierspacing = 0.1 pme_order = 5 ewald_rtol = 1e-5 ; --------------------------- ; Berendsen temperature and preasure coupling Tcoupl = berendsen tc-grps = DPPC SOL tau_t = 0.6 0.6 ; i have also tried a tau value of 0.1, but no speed up ref_t = 323.0 323.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; --------------------------- gen_vel = yes gen_temp = 323.0 gen_seed = 194040 ;########################################### -- Maria G. Technical University of Denmark Copenhagen
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