[gmx-users] GMX TRJCONV ERROR and GMX CHECK ERROR

[Budheswar Dehury]

Dear All,

Can anybody suggest what should be ideal solution for this the blow mentioned two errors using gmx trjconv and gmx check error in GROMACS 2018.4


GROMACS:      gmx trjconv, version 2018.3-dev-20181031-cfa1b1c
Executable:   /apps/gromacs/gromacs-2018.4-git/bin/gmx
Data prefix:  /apps/gromacs/gromacs-2018.4-git
Working dir:  /run/media/bude/Data/BD/S_OPEN/SOpen/WILDTYPE/Seed3
Command line:
  gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md.xtc -pbc mol -ur compact

Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file md_0_1.tpr, VERSION 2018.2 (single precision)
Reading file md_0_1.tpr, VERSION 2018.2 (single precision)

-------------------------------------------------------
Program:     gmx trjconv, version 2018.3-dev-20181031-cfa1b1c
Source file: src/gromacs/topology/symtab.cpp (line 137)

Fatal error:
symtab get_symtab_handle 21279775 not found



and


GROMACS:      gmx check, version 2018.3-dev-20181031-cfa1b1c
Executable:   /apps/gromacs/gromacs-2018.4-git/bin/gmx
Data prefix:  /apps/gromacs/gromacs-2018.4-git
Working dir:  /run/media/bude/Data/BD/S_OPEN/SOpen/WILDTYPE/Seed3
Command line:
  gmx check -f md_0_1.xtc

Checking file md_0_1.xtc
Reading frame       0 time    0.000
# Atoms  235013
Precision 0.001 (nm)
Reading frame       1 time   20.000   Warning at frame 1: there are 17527 particles with all coordinates zero

-------------------------------------------------------
Program:     gmx check, version 2018.3-dev-20181031-cfa1b1c
Source file: src/gromacs/fileio/xtcio.cpp (line 91)

Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)


The log file displays log statistics without any error while I tried to analyze it says the following errors.


I need your valuable suggestion and guidance.

Thanking You
With Warm Regards

Budheswar