Dear All, My apologies. I had too big a simulation cell, and too few atoms, hence the problem.
No particular reason to choose order 5. I will try with pme_order 4 and see if it improves performance anyway. thanks ! -maria On Mon, Mar 24, 2008 at 2:19 PM, Carsten Kutzner <[EMAIL PROTECTED]> wrote: > Am 24.03.2008 um 10:17 schrieb maria goranovic: > > > 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 ? > Is there a special reason for using pme_order=5? I would use the > default, 4 instead, or at least an even number. > > Carsten > > > 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 _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Maria G. Technical University of Denmark Copenhagen
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