[gmx-users] question

[Andrew Bostick]

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