Hello, I merged two simulation boxes, and now I want to perform a minimization to remove the problems at their boundary! I have reduced the dt to 0.000000001 and emstep to 0.000000001 as well. But still I get the message Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision) Making 1D domain decomposition 8 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.00000e-05 Number of steps = 705032704
t = 0.000 ps: Water molecule starting at atom 190501 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates ------------------------------------------------------- Program mdrun_d_mpi, VERSION 4.0.5 Source code file: pme.c, line: 518 Fatal error: 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group as part of my error message. Should I still reduce the mentioned parameters? Regards, Payman _______________________________________________ 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/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/mailing_lists/users.php
