gromacs 4.5.1 On Fri, Jan 28, 2011 at 12:40 PM, Erik Marklund <er...@xray.bmc.uu.se>wrote:
> PME is still an Ewald sum. > > Erik > > Denny Frost skrev 2011-01-28 20.38: > > 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 >> > > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755er...@xray.bmc.uu.se > http://folding.bmc.uu.se/ > > > -- > 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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