[gmx-users] Error in gmx trjcat

Tue Apr 17 13:06:09 CEST 2018

Hey all,

I'm experiencing an error while using trjcat command. Initially, I ran
a simulation for 50 ns and then extended till 100ns. After extension,
I concatenated the trajectories of both the runs using gmx trjcat.

Then, again I extended the run from 100 ns to 500 ns. Finally, I tried
to concatenate the previously concatenated 100 ns trajectory file with
the final (500 ns) trajectory. This step yielded an error (pasted
below).

GROMACS:      gmx trjcat, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx trjcat -f 100cat.xtc new2.xtc -o cat500.xtc

Reading frame       1 time 100010.000

Summary of files and start times used:

          File                Start time       Time step
---------------------------------------------------------
               100cat.xtc        0.000 ps       10.000 ps
                 new2.xtc   100000.000 ps       10.000 ps

Reading frame       0 time    0.000

Continue writing frames from 100cat.xtc t=0 ps, frame=0
Last frame      10000 time 100000.000   ->  frame   9000 time 90000.000 ps
Reading frame       0 time 100000.000
lasttime 99990

Continue writing frames from new2.xtc t=100000 ps, frame=10000
*** Error in `gmx': munmap_chunk(): invalid pointer:
0x0000000001455380 ***s
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f929a9a07e5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7f929a9ad698]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(xdr3dfcoord+0x1387)[0x7f929b9b31d7]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_xtc+0x1bd)[0x7f929b9d539d]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_frame+0x267)[0x7f929b9d1977]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_trjcat+0x32c2)[0x7f929bb64842]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7f929b74a4c4]
gmx(main+0x8c)[0x40c98c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f929a949830]
gmx(_start+0x29)[0x40cb19]
======= Memory map: ========
00400000-0043d000 r-xp 00000000 08:07 2646598
  /usr/local/gromacs/bin/gmx
0063c000-0063d000 r--p 0003c000 08:07 2646598
  /usr/local/gromacs/bin/gmx
0063d000-0063e000 rw-p 0003d000 08:07 2646598
  /usr/local/gromacs/bin/gmx
0063e000-0063f000 rw-p 00000000 00:00 0
013f8000-014b7000 rw-p 00000000 00:00 0                                  [heap]
7f929a0de000-7f929a0ff000 r-xp 00000000 08:07 2098798
  /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f929a0ff000-7f929a2fe000 ---p 00021000 08:07 2098798
  /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f929a2fe000-7f929a2ff000 r--p 00020000 08:07 2098798
  /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f929a2ff000-7f929a300000 rw-p 00021000 08:07 2098798
  /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f929a300000-7f929a318000 r-xp 00000000 08:07 2623397
  /lib/x86_64-linux-gnu/libpthread-2.23.so
7f929a318000-7f929a517000 ---p 00018000 08:07 2623397
  /lib/x86_64-linux-gnu/libpthread-2.23.so
7f929a517000-7f929a518000 r--p 00017000 08:07 2623397
  /lib/x86_64-linux-gnu/libpthread-2.23.so
7f929a518000-7f929a519000 rw-p 00018000 08:07 2623397
  /lib/x86_64-linux-gnu/libpthread-2.23.so
7f929a519000-7f929a51d000 rw-p 00000000 00:00 0
7f929a51d000-7f929a524000 r-xp 00000000 08:07 2639498
  /lib/x86_64-linux-gnu/librt-2.23.so
7f929a524000-7f929a723000 ---p 00007000 08:07 2639498
  /lib/x86_64-linux-gnu/librt-2.23.so
7f929a723000-7f929a724000 r--p 00006000 08:07 2639498
  /lib/x86_64-linux-gnu/librt-2.23.so
7f929a724000-7f929a725000 rw-p 00007000 08:07 2639498
  /lib/x86_64-linux-gnu/librt-2.23.so
7f929a725000-7f929a728000 r-xp 00000000 08:07 2623462
  /lib/x86_64-linux-gnu/libdl-2.23.so
7f929a728000-7f929a927000 ---p 00003000 08:07 2623462
  /lib/x86_64-linux-gnu/libdl-2.23.so
7f929a927000-7f929a928000 r--p 00002000 08:07 2623462
  /lib/x86_64-linux-gnu/libdl-2.23.so
7f929a928000-7f929a929000 rw-p 00003000 08:07 2623462
  /lib/x86_64-linux-gnu/libdl-2.23.so
7f929a929000-7f929aae9000 r-xp 00000000 08:07 2623402
  /lib/x86_64-linux-gnu/libc-2.23.so
7f929aae9000-7f929ace9000 ---p 001c0000 08:07 2623402
  /lib/x86_64-linux-gnu/libc-2.23.so
7f929ace9000-7f929aced000 r--p 001c0000 08:07 2623402
  /lib/x86_64-linux-gnu/libc-2.23.so
7f929aced000-7f929acef000 rw-p 001c4000 08:07 2623402
  /lib/x86_64-linux-gnu/libc-2.23.so
7f929acef000-7f929acf3000 rw-p 00000000 00:00 0
7f929acf3000-7f929ad09000 r-xp 00000000 08:07 2626206
  /lib/x86_64-linux-gnu/libgcc_s.so.1
7f929ad09000-7f929af08000 ---p 00016000 08:07 2626206
  /lib/x86_64-linux-gnu/libgcc_s.so.1
7f929af08000-7f929af09000 rw-p 00015000 08:07 2626206
  /lib/x86_64-linux-gnu/libgcc_s.so.1
7f929af09000-7f929b011000 r-xp 00000000 08:07 2621457
  /lib/x86_64-linux-gnu/libm-2.23.so
7f929b011000-7f929b210000 ---p 00108000 08:07 2621457
  /lib/x86_64-linux-gnu/libm-2.23.so
7f929b210000-7f929b211000 r--p 00107000 08:07 2621457
  /lib/x86_64-linux-gnu/libm-2.23.so
7f929b211000-7f929b212000 rw-p 00108000 08:07 2621457
  /lib/x86_64-linux-gnu/libm-2.23.so
7f929b212000-7f929b384000 r-xp 00000000 08:07 2100941
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f929b384000-7f929b584000 ---p 00172000 08:07 2100941
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f929b584000-7f929b58e000 r--p 00172000 08:07 2100941
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f929b58e000-7f929b590000 rw-p 0017c000 08:07 2100941
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f929b590000-7f929b594000 rw-p 00000000 00:00 0
7f929b594000-7f929c8e1000 r-xp 00000000 08:07 2646399
  /usr/local/gromacs/lib/libgromacs.so.1.4.0
7f929c8e1000-7f929cae0000 ---p 0134d000 08:07 2646399
  /usr/local/gromacs/lib/libgromacs.so.1.4.0
7f929cae0000-7f929caff000 r--p 0134c000 08:07 2646399
  /usr/local/gromacs/lib/libgromacs.so.1.4.0
7f929caff000-7f929cb21000 rw-p 0136b000 08:07 2646399
  /usr/local/gromacs/lib/libgromacs.so.1.4.0
7f929cb21000-7f929cb2b000 rw-p 00000000 00:00 0
7f929cb2b000-7f929cb51000 r-xp 00000000 08:07 2623394
  /lib/x86_64-linux-gnu/ld-2.23.so
7f929cd27000-7f929cd30000 rw-p 00000000 00:00 0
7f929cd4e000-7f929cd50000 rw-p 00000000 00:00 0
7f929cd50000-7f929cd51000 r--p 00025000 08:07 2623394
  /lib/x86_64-linux-gnu/ld-2.23.so
7f929cd51000-7f929cd52000 rw-p 00026000 08:07 2623394
  /lib/x86_64-linux-gnu/ld-2.23.so
7f929cd52000-7f929cd53000 rw-p 00000000 00:00 0
7ffc2b427000-7ffc2b448000 rw-p 00000000 00:00 0                          [stack]
7ffc2b4dc000-7ffc2b4df000 r--p 00000000 00:00 0                          [vvar]
7ffc2b4df000-7ffc2b4e1000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
  [vsyscall]
Aborted (core dumped)

How do I overcome the error and concatenate the files?

Best,
Azeem