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  • GROMACS
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  • #3653
Closed
Open
Created Sep 08, 2020 by Daniel Winter@winterdl

gmx trjcat -demux command causes fatal error with default output

Hello,

I’ve used GROMACS to perform a short REMD simulation (200 ps) in order to test whether my choice of temperature range allowed sufficient exchanges between replicas.

The REMD simulations progressed and finished without problems and produced the following files in each replica directory: remd.part0001.log, remd.part0001.xtc, remd.part0001.edr, remd.part0001.trr, remd.part0001.gro using -deffnm remd and -noappend to run the REMD simulation. There were 17 directories named rep_0 to rep_16. Note that I was in a separate directory to create the new files, hence going up one directory with cat ../rep_{0..16}/

Concatenating the .part0001.log files with the command cat ../rep_{0..16}/remd.part0001.log > REMD.log works fine and so does demux.pl REMD.log command to create the replica_index.xvg and replica_temp.xvg files.

However, demultiplexing the .xtc or .trr files with gmx trjcat -f ../rep_{0..16}/remd.part0001.xtc -demux replica_index.xvg causes the following error (which also occurs if -o trajout.xtc or any output name is specified):

Command line:
gmx trjcat -f ../rep_0/remd.part0001.xtc ../rep_1/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 ../rep_8/remd.part0001.xtc ../rep_9/remd.part0001.xtc ..
/rep_10/remd.part0001.xtc ../rep_11/remd.part0001.xtc ../rep_12/remd.part0001.xtc ../rep_13/remd.part0001.xtc ../rep_14/remd.part0001.xtc ../rep_15/remd.part0001.xtc ../rep_16/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
-------------------------------------------------------
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

However, the command gmx trjcat -f ../rep_{0..16}/remd.part0001.trr -demux replica_index.xvg -o {0..16}_trajout.xtc where all output names are specified works:

Command line:
gmx trjcat -f ../rep_0/remd.part0001.xtc ../rep_1/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 ../rep_8/remd.part0001.xtc ../rep_9/remd.part0001.xtc ../rep_10/remd.part0001.xtc ../rep
_11/remd.part0001.xtc ../rep_12/remd.part0001.xtc ../rep_13/remd.part0001.xtc ../rep_14/remd.part0001.xtc ../rep_15/remd.part0001.xtc ../rep_16/remd.part0001.xt
c -demux replica_index.xvg -o 0_trajout.xtc 1_trajout.xtc 2_trajout.xtc 3_trajout.xtc 4_trajout.xtc 5_trajout.xtc 6_trajout.xtc 7_trajout.xtc 8_trajout.xtc 9_tr
ajout.xtc 10_trajout.xtc 11_trajout.xtc 12_trajout.xtc 13_trajout.xtc 14_trajout.xtc 15_trajout.xtc 16_trajout.xtc

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

Last frame 20 time 200.000

GROMACS reminds you: “I love fools’ experiments. I am always making them.” (Charles Darwin)

The error occurs (and the solution solution works) for both .xtc or .trr files as input. I've uploaded the 17 trajectories (renamed remd_{0..16}.xtc) and replica_index.xvg file if this can assist troubleshooting.

remd_13.xtc

remd_14.xtc

remd_15.xtc

remd_16.xtc

replica_index.xvg

remd_0.xtc

remd_1.xtc

remd_2.xtc

remd_3.xtc

remd_4.xtc

remd_5.xtc

remd_6.xtc

remd_7.xtc

remd_8.xtc

remd_9.xtc

remd_10.xtc

remd_11.xtc

remd_12.xtc

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