> > Here's your problem. You have pairs defined that are in excess of 12 nm, > but they are assigned to a 1-4 interaction, so atoms that should be > separated by three bonds. The user-defined potential shouldn't matter > here unless you've added [pairs] to the topology. > > I see your point. What can I do to define LJ potential between two atoms which are actually far apart? and the results from the single processors are correct? I tried it in a different way too, I generated tables between pairs which are far apart (with the LJ potential) and kept them in the bonded section with function type 8 (to exclude LJ from usual force field). The system has 12282 number of particles and the size of the box is 9.76580 11.92760 11.62620. I minimized energy with 10 processors and -rdd 1.4. It worked. In NVT equilibration I am getting the following error:
Atom distribution over 8 domains: av 1535 stddev 38 min 1508 max 1582 Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Tab. Bonds of 818 missing 16 ------------------------------------------------------- Program: gmx mdrun, version 2018.6 Source file: src/gromacs/domdec/domdec_topology.cpp (line 240) MPI rank: 0 (out of 8) Software inconsistency error: Some interactions seem to be assigned multiple times -- 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.