Hi Gábor, Without more details (and little experience with martini systems) I can suggest: tweaking DD so you don't end up with a too small box wrt the number of cells by: - Changing the number of ranks by using less/more cores to get a convenient decomposition; I assume you had 6x4x4 before on 96 cores, so you can try using e.g. 80 cores which will give you a 5x4x4 DD grid; - Use OpenMP: your 6x4x4 DD with 1 OpenMP thread/rank will become 4x3x4 with 2 threads/rank.
Cheers, -- Szilárd On Wed, Sep 23, 2015 at 2:54 PM, Gábor Balogh <gaborbalog...@gmail.com> wrote: > Hello. > I am trying to simulate a multi-domain protein using the Martini > coarse-grained force field. The system consists of ~1600 protein "atoms" > and ~26000 Martini water "beads". The water box is large compared to the > size of the protein because of the significant conformational changes. The > protein has an elastic network with the following parameters: lower cutoff: > 0.5 nm, upper cutoff: 0.9 nm, force constant: 500 kJ/(mol*nm). Elastic > "bonds" between atoms in two different domains were removed. > > The MD parameters are similar to this: > > http://cgmartini.nl/cgmartini/images/parameters/exampleMDP/martini_v2.x_new-rf.mdp > > My first simulation was running on a supercomputer, 96 CPU cores. The > simulation crashed after ~2760000 steps: > > A list of missing interactions: > Harmonic Pot. of 2821 missing 1 > > Molecule type 'Protein' > the first 10 missing interactions, except for exclusions: > Harmonic Pot. atoms 1098 1306 global 1098 1306 > Fatal error: > 1 of the 8124 bonded interactions could not be calculated because some > atoms involved moved further apart than the multi-body cut-off distance > (1.317 nm) or the two-body cut-off distance (1.317 nm), see option -rdd, > for pairs and tabulated bonds also see option -ddcheck > > Second simulation (-rdd was set to 1.6, 72 CPU cores) crashed after > ~70170000 steps: > > Fatal error: > The X-size of the box (9.696262) times the triclinic skew factor (0.990125) > is smaller than the number of DD cells (6) times the smallest allowed cell > size (1.600000) > > Third simulation (rdd=1.5, 48 CPU cores) crashed after 24939840 steps: > > Step 24939840: The domain decomposition grid has shifted too much in the > Y-direction around cell 2 3 0 (2 3 2, 3 3 0, 1 3 1, 2 3 1, 3 3 1, 1 3 2, 3 > 3 2, 1 3 0, 0 3 0, 0 3 2, 0 3 1). This should not have happened. Running > with less nodes might avoid this issue. (12 error messages). > > What MD/domain decomposition parameters should I use? > > Thanks in advance. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
