Hi Folks,<br><br>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). <br>
<br>Can anybody suggest why this is happening ? Is it because of latency in the cpu communication? If so, what is the workaround ? <br><br>My .mdp script is below.<br>These are the run commands.<br><br>grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o heat.tpr<br>
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<br><br>;###########################################<br>; heat.mdp<br>;<br>title = heating<br>
cpp = /usr/bin/cpp<br>constraints = hbonds<br>constraint_algorithm = lincs<br>unconstrained_start = yes<br>integrator = md<br>nsteps = 25000<br>dt = 0.002<br>
comm_mode = linear<br>nstxout = 5000<br>nstvout = 5000<br>nstlog = 5000<br>nstenergy = 5000<br>nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>
; ------------------<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rlist = 1.0<br>rvdw = 1.0<br>fourierspacing = 0.1<br>pme_order = 5<br>
ewald_rtol = 1e-5<br>; ---------------------------<br>; Berendsen temperature and preasure coupling<br>Tcoupl = berendsen<br>tc-grps = DPPC SOL<br>tau_t = 0.6 0.6<br>
; i have also tried a tau value of 0.1, but no speed up<br>ref_t = 323.0 323.0<br>Pcoupl = berendsen<br>Pcoupltype = semiisotropic<br>tau_p = 1.0 1.0<br>compressibility = 4.5e-5 4.5e-5<br>
ref_p = 1.0 1.0<br>; ---------------------------<br>gen_vel = yes<br>gen_temp = 323.0<br>gen_seed = 194040<br>;###########################################<br><br>
-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen