I don't have any domain decomposition information like that in my log file. That's worrisome. The only other information I could find about PME and Ewald and this set of lines:
Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 4400 data points for Ewald. Tabscale = 2000 points/nm Generated table with 4400 data points for LJ6. Tabscale = 2000 points/nm Generated table with 4400 data points for LJ12. Tabscale = 2000 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. Why does it say it will do PME on one line, then ordinary Ewald later? On Fri, Jan 28, 2011 at 12:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Denny Frost wrote: > >> I just realized that that was a very old mdp file. Here is an mdp file >> from my most recent run as well as what I think are the domain decomposition >> statistics. >> >> mdp file: >> title = BMIM+PF6 >> cpp = /lib/cpp >> constraints = hbonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 4000000 ; total 8ns. >> nstcomm = 1 >> nstxout = 50000 >> nstvout = 50000 >> nstfout = 0 >> nstlog = 5000 >> nstenergy = 5000 >> nstxtcout = 25000 >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> coulombtype = PME >> vdwtype = Cut-off >> rlist = 1.2 >> rcoulomb = 1.2 >> rvdw = 1.2 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = berendsen >> tc_grps = BMI PF6 tau_t = 0.2 0.2 >> ref_t = 300 300 >> nsttcouple = 1 >> ; Energy monitoring >> energygrps = BMI PF6 >> ; Isotropic pressure coupling is now on >> Pcoupl = berendsen >> pcoupltype = isotropic >> ;pc-grps = BMI PFF >> tau_p = 1.0 >> ref_p = 1.0 >> compressibility = 4.5e-5 >> >> ; Generate velocites is off at 300 K. >> gen_vel = yes >> gen_temp = 300.0 >> gen_seed = 100000 >> >> domain decomposition >> There are: 12800 Atoms >> Max number of connections per atom is 63 >> Total number of connections is 286400 >> Max number of graph edges per atom is 6 >> Total number of graph edges is 24800 >> >> > More useful information is contained at the very top of the .log file, > after the citations. An example from one of my own runs is: > > Linking all bonded interactions to atoms > There are 2772 inter charge-group exclusions, > will use an extra communication step for exclusion forces for PME > > The initial number of communication pulses is: X 2 Y 1 > The initial domain decomposition cell size is: X 1.05 nm Y 1.58 nm > > The maximum allowed distance for charge groups involved in interactions is: > non-bonded interactions 1.400 nm > (the following are initial values, they could change due to box > deformation) > two-body bonded interactions (-rdd) 1.400 nm > multi-body bonded interactions (-rdd) 1.054 nm > atoms separated by up to 5 constraints (-rcon) 1.054 nm > > When dynamic load balancing gets turned on, these settings will change to: > The maximum number of communication pulses is: X 2 Y 2 > The minimum size for domain decomposition cells is 0.833 nm > The requested allowed shrink of DD cells (option -dds) is: 0.80 > The allowed shrink of domain decomposition cells is: X 0.79 Y 0.53 > The maximum allowed distance for charge groups involved in interactions is: > non-bonded interactions 1.400 nm > two-body bonded interactions (-rdd) 1.400 nm > multi-body bonded interactions (-rdd) 0.833 nm > atoms separated by up to 5 constraints (-rcon) 0.833 nm > > > Making 2D domain decomposition grid 9 x 6 x 1, home cell index 0 0 0 > > > Also, the output under "DOMAIN DECOMPOSITION STATISTICS" (at the bottom of > the file) would be useful. Also look for any notes about performance lost > due to imbalance, waiting for PME, etc. These provide very detailed clues > about how your system was treated. > > -Justin > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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