Dear gromacs users,
I tried using trjcat like this:
trjcat -f gromacs*.trr -demux replica_index.xvg (see below for
replica_index.xvg and logfile)
there are 20 trajectories containing each 2001 frames, with timestep of
0.5ps (I checked it with gmxcheck).
The error:
Reading frame 60 time 1.500 Segmentation fault
(frame doesn't fit with the time...)
this is my replica_index.xvg file (it contains, 2001 lines with timestep of
0.5ps):
0 0 1 2 3 4 5 6 7 8 9 10 11 12
13 14 15 16 17 18 19
0.5 0 1 3 4 2 5 6 7 9 10 8 11 12
13 14 16 15 17 19 18
.
.
.
.
999.5 12 0 6 1 4 3 8 5 18 9 13 16 2
10 17 7 11 19 15 14
1000.0 12 0 6 1 4 3 8 5 18 9 13 16 2
10 17 7 11 19 15 14
This is the logfile:
:-) trjcat (-:
Option Filename Type Description
------------------------------------------------------------
-f gromacs20.trr Input, Mult.
gromacs210.trr
gromacs211.trr
gromacs212.trr
gromacs213.trr
gromacs214.trr
gromacs215.trr
gromacs216.trr
gromacs217.trr
gromacs218.trr
gromacs219.trr
gromacs21.trr
gromacs22.trr
gromacs23.trr
gromacs24.trr
gromacs25.trr
gromacs26.trr
gromacs27.trr
gromacs28.trr
gromacs29.trr Generic trajectory: xtc trr trj gro g96
pdb
-o trajout.xtc Output, Mult. Generic trajectory: xtc trr trj gro g96
pdb
-n index.ndx Input, Opt. Index file
-demux replica_index.xvg Input, Opt! xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-b time -1 First time to use (ps)
-e time -1 Last time to use (ps)
-dt time 0 Only write frame when t MOD dt = first time (ps)
-prec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]settime bool no Change starting time interactively
-nrepl int 1 Number of replicas assumed to be numbered
consecutively. Only used with the -demux option
-[no]sort bool yes Sort trajectory files (not frames)
-[no]keeplast bool no keep overlapping frames at end of trajectory
-[no]cat bool no do not discard double time frames
Read 20 sets of 2000 points, dt = 0.5
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Reading frame 60 time 1.500 Segmentation fault
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