Is tpbconv with the "pbc" option the best way to make the molecules whole again?
On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Denny Frost wrote: > >> This run is actually a combination of two 5x5x5 nm boxes, one if which was >> previously run in DD, and the other is water. Since the length of that bond >> is almost 5 nm, is it possible that the pbc's are not being recognized? >> There is no way I have a bond that long from my previous run. >> >> > I'll venture a guess that there were broken molecules in the system you > concatenated? That would gel with a bond that stretches across a 5-nm box. > You have to deal with whole molecules in the input configuration. > > -Justin > > On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Denny Frost wrote: >> >> I'm using version 4.5.3 >> >> Here's the output from the log file from DD initiation to the >> error: >> >> Initializing Domain Decomposition on 8 nodes >> Dynamic load balancing: auto >> Will sort the charge groups at every domain (re)decomposition >> Initial maximum inter charge-group distances: >> two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996 >> multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997 >> Minimum cell size due to bonded interactions: 5.382 nm >> >> >> Bonded interactions should normally not occur over such a length. >> The information printed here points to the culprits. What are >> these atoms, and why are they bonded if they are so far away? >> >> -Justin >> >> Using 0 separate PME nodes >> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 >> Optimizing the DD grid for 8 cells with a minimum initial size >> of 6.728 nm >> The maximum allowed number of cells is: X 0 Y 0 Z 1 >> >> ------------------------------------------------------- >> Program mdrun_mpi, VERSION 4.5.3 >> Source code file: domdec.c, line: 6428 >> >> Fatal error: >> There is no domain decomposition for 8 nodes that is compatible >> with the given box and a minimum cell size of 6.72787 nm >> Change the number of nodes or mdrun option -rdd or -dds >> Look in the log file for details on the domain decomposition >> For more information and tips for troubleshooting, please check >> the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> And here is my mdp file >> >> title = BMIM+PF6 >> cpp = /lib/cpp >> constraints = hbonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 75000 ; total 150 ps >> nstcomm = 10 >> 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 SOL tau_t >> = 0.2 0.2 0.2 >> ref_t = 300 300 300 >> nsttcouple = 1 >> ; Energy monitoring >> energygrps = BMI PF6 SOL >> ; Isotropic pressure coupling is now on >> Pcoupl = berendsen >> pcoupltype = isotropic >> ;pc-grps = BMI PFF >> tau_p = 2.0 >> 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 Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Denny Frost wrote: >> >> I am trying to start a run using domain decomposition on a >> 5x5x10 nm box with about 26,000 atoms in it. I've tried >> running >> 8-16 pp nodes, but gromacs always throws an error saying >> that >> there is no domain decomposition compatible with this box >> and a >> minimum cell size of 6.728 nm. I've tried many values >> for -dds >> and a few dd vectors, but with no luck. Does anyone know >> to get >> domain decomposition working on a rectangular system like >> this? >> >> >> Not without significantly more information. Please post: >> >> 1. Your Gromacs version >> 2. Any DD-related information that is printed to either the >> log file >> or stdout >> 3. Your .mdp file >> >> -Justin >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto: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> >> <mailto: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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- 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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