when you use gmx trjcat you need to call the files only once. I mean, in your case, for instance would be:

gmx trjcat -f ../rep_*/remd.part0001.xtc

try this and let me know if you solve your problem

Cheers

Hello Florencia,

The command you suggested is still interpreted as calling a series of files after -f and generates the same result:

gmx trjcat -f ../rep_*/remd.part0001.xtc -demux replica_index.xvg

Results in:

Command line:

gmx trjcat -f ../rep_0/remd.part0001.xtc ../rep_1/remd.part0001.xtc ../rep_10/remd.part0001.xtc ../rep_11/remd.part0001.xtc ../rep_12/remd.par

t0001.xtc ../rep_13/remd.part0001.xtc ../rep_14/remd.part0001.xtc ../rep_15/remd.part0001.xtc ../rep_16/remd.part0001.xtc ../rep_2/remd.part0001

.xtc ../rep_3/remd.part0001.xtc ../rep_4/remd.part0001.xtc ../rep_5/remd.part0001.xtc ../rep_6/remd.part0001.xtc ../rep_7/remd.part0001.xtc ../r

ep_8/remd.part0001.xtc ../rep_9/remd.part0001.xtc -demux replica_index.xvg

Note that major changes are planned in future for trjcat, to improve usability and utility.Read 17 sets of 1684 points, dt = 0.117647

Reading frame 0 time 0.000

Back Off! I just backed up 16_trajout.xtc to ./#16_trajout.xtc.2#

-------------------------------------------------------

Program: gmx trjcat, version 2020.1

Source file: src/gromacs/fileio/trxio.cpp (line 557)

Fatal error:

Sorry, write_trxframe can not write unknown

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------

In addition, if I were to call only one .xtc file, there is an input error that requests more input files:

gmx trjcat -f ../rep_0/remd.part0001.xtc -demux replica_index.xvg

Results in:

Command line:

gmx trjcat -f ../rep_0/remd.part0001.xtc -demux replica_index.xvg

Note that major changes are planned in future for trjcat, to improve usability and utility.Read 17 sets of 1684 points, dt = 0.117647

-------------------------------------------------------

Program: gmx trjcat, version 2020.1

Source file: src/gromacs/tools/trjcat.cpp (line 556)

Fatal error:

You have specified 1 files and 17 entries in the demux table

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------

Have you used trjcat in the context of demultiplexing REMD simulations? Was there a particular way you organised your files for those commands to work? Recent versions of GROMACS request each replica .tpr file to be generated in a separate directory, where the outputs will be saved for each replica (that was not the case for older versions of GROMACS). But perhaps after the REMD simulation the files must be rearranged?

It appears -demux works by specifying all input AND all output file names, as such:

gmx trjcat -f …/rep_{0..16}/remd.part0001.trr -demux replica_index.xvg -o {0..16}_trajout.xtc

It is unclear to me why it is necessary, since without using the -o flag, or using -o trajout.xtc, GROMACS attempts to generate different outputs (a file named 16_trajout.xtc starts being created before the fatal error).

Clearly GROMACS is coded to generate one output per input, but the curent version fails if you don't specify the output file names manually.

I have yet to look into all 17 output files to make sure the correct concatenations were created.