Dear gromacs users I am doing md simulation of rna-ligand system using gromacs 5.0.5.
In equilibration phase (NVT), I encountered with following error? GROMACS: gmx mdrun, VERSION 5.0.5 Executable: /share/apps/gromacs/bin/gmx Library dir: /share/apps/gromacs/share/gromacs/top Command line: gmx mdrun -nt 8 -v -deffnm nvt Back Off! I just backed up nvt.log to ./#nvt.log.4# Reading file nvt.tpr, VERSION 5.0.5 (single precision) Changing nstlist from 10 to 25, rlist from 1.4 to 1.437 Using 1 MPI thread Using 8 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Back Off! I just backed up nvt.trr to ./#nvt.trr.4# Back Off! I just backed up nvt.edr to ./#nvt.edr.4# Double sids (704, 705) for atom 2525 Double sids (704, 705) for atom 2526 Double sids (704, 705) for atom 2527 Double sids (704, 705) for atom 2528 Double sids (704, 705) for atom 2529 Double sids (704, 705) for atom 2530 Double sids (704, 705) for atom 2531 Double sids (704, 705) for atom 2532 Double sids (704, 705) for atom 2533 Double sids (704, 705) for atom 2534 Double sids (704, 705) for atom 2535 Double sids (704, 705) for atom 2536 Double sids (704, 705) for atom 2537 Double sids (704, 705) for atom 2538 Double sids (704, 705) for atom 2539 Double sids (704, 705) for atom 2540 Double sids (704, 705) for atom 2541 Double sids (704, 705) for atom 2542 Double sids (704, 705) for atom 2543 Double sids (704, 705) for atom 2544 Double sids (704, 705) for atom 2545 Double sids (704, 705) for atom 2546 Double sids (704, 705) for atom 2547 Double sids (704, 705) for atom 2548 Double sids (704, 705) for atom 2549 Double sids (704, 705) for atom 2550 ------------------------------------------------------- Program gmx, VERSION 5.0.5 Source code file: /export/apps/gromacs/gromacs-5.0.5/src/gromacs/gmxlib/invblock.c, line: 98 Fatal error: Double entries in block structure. Item 1586 is in blocks 705 and 704 Cannot make an unambiguous inverse block. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ----------------------------------------------------------------------------------------------- How to solve this problem? Any help will highly appreciated -- 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.