[gmx-users] trjcat accepts only binary formats

[András Ferenc WACHA]

Dear Gromacs Developers,

I have found that in version 2018 the trjcat program stopped supporting
.gro as an input file for the switch "-f". I have been using this
feature to concatenate several coordinate states to calculate single
point energy with gmx mdrun -rerun.

I have found a workaround to first convert the .gro files to .trr (or
.xtc) and then concatenate them, but I find that really clumsy.
Incidentally, I have also found that if I issue gmx trjconv -f
grofile.gro -o trajectory.trr (i.e. without specifying the tpr file with
-s) segfaults. If the tpr is specified, the program runs correctly and a
binary file is produced.

Do you have a better solution for this?

Thank you,

Andras Wacha

PS: The relevant output of "gmx -version" is:

GROMACS version:    2018
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        disabled
SIMD instructions:  SSE4.1
FFT library:        fftw-3.3.5-sse2
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      hwloc-1.11.0
Tracing support:    disabled
Built on:           2018-01-14 15:27:50
Built by:           wachaandras at flambeau [CMAKE]
Build OS/arch:      Linux 4.14.13-1-ARCH x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Core(TM) i5 CPU       M 520  @ 2.40GHz
Build CPU family:   6   Model: 37   Stepping: 5
Build CPU features: aes apic clfsh cmov cx8 cx16 htt intel lahf mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
ssse3
C compiler:         /usr/sbin/gcc-6 GNU 6.4.1
C compiler flags:    -msse4.1   -march=native -O2 -pipe
-fstack-protector-strong  -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast 
C++ compiler:       /usr/sbin/g++-6 GNU 6.4.1
C++ compiler flags:  -msse4.1   -march=native -O2 -pipe
-fstack-protector-strong -std=c++11   -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast 


-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu, 
CREDO SAXS instrument: http://credo.ttk.mta.hu

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