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 On Thu, Jan 27, 2011 at 4:32 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Denny Frost wrote: > >> about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband. Below is a copy >> of my mdp file. >> >> title = BMIM+PF6 >> cpp = /lib/cpp >> constraints = all_bonds >> integrator = md >> dt = 0.004 ; ps ! >> nsteps = 20000000 ; total 4ns. >> nstcomm = 1 >> nstxout = 50000 >> nstvout = 50000 >> nstfout = 0 >> nstlog = 5000 >> nstenergy = 5000 >> nstxtcout = 25000 >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> coulombtype = PME >> vdwtype = Shift >> rlist = 1.0 >> rcoulomb = 1.0 >> rvdw = 1.0 >> fourierspacing = 0.6 >> > > This fourierspacing is 5-6 times larger than what is normally accepted as > sufficiently accurate. A sparse grid will make the PME algorithm faster, > actually, but at the expense of accuracy. > > Can you post the domain decomposition statistics from the .log file? They > appear just above the energies from time 0. What did grompp tell you about > the relative PME:PP load? > > -Justin > > ;pme_order = 4 >> ewald_rtol = 1e-5 >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = berendsen >> tc_grps = BMI PF6 tau_t = 0.1 0.1 >> 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 >> >> >> On Thu, Jan 27, 2011 at 4:12 PM, Dallas Warren >> <dallas.war...@monash.edu<mailto: >> dallas.war...@monash.edu>> wrote: >> >> You will need to provide more details on the system. How many >> atoms, what sort of computer system is it being run on, how many >> nodes, copy of the mdp file etc. >> >> >> Catch ya, >> >> Dr. Dallas Warren >> >> Medicinal Chemistry and Drug Action >> >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3010 >> dallas.war...@monash.edu <mailto:dallas.war...@monash.edu> >> >> >> +61 3 9903 9304 >> --------------------------------- >> When the only tool you own is a hammer, every problem begins to >> resemble a nail. >> >> >> *From:* gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org> >> [mailto:gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org>] *On Behalf Of *Denny Frost >> *Sent:* Friday, 28 January 2011 9:34 AM >> *To:* Discussion list for GROMACS users >> *Subject:* [gmx-users] Slow Runs >> >> >> I am taking over a project for a graduate student who did MD using >> Gromacs 3.3.3. I now run similar simulations with Gromacs 4.5.1 and >> find that they run only about 1/2 to 1/3 as fast as the previous >> runs done in Gromacs 3.3.3. The runs have about the same number of >> atoms and both use opls force fields. The mdp files is virtually >> the same (I copied them). The only major difference is that my runs >> have difference species and thus have different (although smaller) >> itp files. The runs are stable and give reasonable thermodynamic >> properties - they're just slow. Has anyone had any experience with >> something like this? >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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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