Problem about 'gmx distance'

User discussions
,
1

GROMACS version:2018.8
GROMACS modification: No
I am using gromacs with Martini force field, and i want to obtain the distribution of bond length. I use command ‘gmx distance’ to compute about 4000 pairs of bond length, which is divided into 2 groups.
PS:I use gromacs with centos7.6 which is installed in a virtual environment.
Here is the error information :

GROMACS: gmx distance, version 2018.8
Executable: /sob/gmx2018.8/bin/gmx
Data prefix: /sob/gmx2018.8
Working dir: /mnt/hgfs/P2VP
Command line:
gmx distance -f NPT_cg.xtc -n bonds.ndx -oh bonds-core.xvg

Available static index groups:
Group 0 “bonds_core” (6400 atoms)
Group 1 “bonds_term” (1600 atoms)
Specify any number of selections for option ‘select’
(Position pairs to calculate distances for):
(one per line, for status/groups, ‘help’ for help, Ctrl-D to end)

0
Selection ‘0’ parsed
Reading frame 0 time 5000.000 *** Error in `gmx’: realloc(): invalid next size: 0x000000000085a0a0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5d4)[0x7f4f2f2355d4]
/lib64/libc.so.6(+0x83bd8)[0x7f4f2f239bd8]
/lib64/libc.so.6(realloc+0x1d2)[0x7f4f2f23b832]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(save_realloc+0x34)[0x7f4f3051fd84]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_Z24gmx_ana_index_make_blockP8t_blockaPK10gmx_mtop_tP15gmx_ana_index_t9e_index_tb+0x1fd)[0x7f4f30832e9d]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(+0x678808)[0x7f4f3085c808]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_Z28gmx_ana_poscalc_set_maxindexP17gmx_ana_poscalc_tP15gmx_ana_index_t+0x18)[0x7f4f3085dd78]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(+0x6409ee)[0x7f4f308249ee]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(+0x6406b0)[0x7f4f308246b0]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx17SelectionCompiler7compileEPNS_19SelectionCollectionE+0x11bf)[0x7f4f30828f4f]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx19SelectionCollection7compileEv+0x80)[0x7f4f3086b0c0]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx23SelectionOptionBehavior15optionsFinishedEv+0x395)[0x7f4f30873775]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx25OptionsBehaviorCollection15optionsFinishedEv+0xcf)[0x7f4f30c1fdcf]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(+0x152031)[0x7f4f30336031]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x1eb)[0x7f4f3033313b]
gmx[0x40dd5c]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f4f2f1d83d5]
gmx[0x40de16]
======= Memory map: ========
00400000-00438000 r-xp 00000000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00637000-00638000 r–p 00037000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00638000-00639000 rw-p 00038000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00639000-0063a000 rw-p 00000000 00:00 0
00817000-00873000 rw-p 00000000 00:00 0 [heap]
7f4f28000000-7f4f28021000 rw-p 00000000 00:00 0
7f4f28021000-7f4f2c000000 —p 00000000 00:00 0
7f4f2e99a000-7f4f2eb99000 r-xp 00000000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f4f2eb99000-7f4f2ed98000 —p 001ff000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f4f2ed98000-7f4f2eda9000 r–p 001fe000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f4f2eda9000-7f4f2edaa000 rw-p 0020f000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f4f2edaa000-7f4f2edb1000 r-xp 00000000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f4f2edb1000-7f4f2efb0000 —p 00007000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f4f2efb0000-7f4f2efb1000 r–p 00006000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f4f2efb1000-7f4f2efb2000 rw-p 00007000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f4f2efb2000-7f4f2efb4000 r-xp 00000000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f4f2efb4000-7f4f2f1b4000 —p 00002000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f4f2f1b4000-7f4f2f1b5000 r–p 00002000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f4f2f1b5000-7f4f2f1b6000 rw-p 00003000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f4f2f1b6000-7f4f2f378000 r-xp 00000000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f4f2f378000-7f4f2f578000 —p 001c2000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f4f2f578000-7f4f2f57c000 r–p 001c2000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f4f2f57c000-7f4f2f57e000 rw-p 001c6000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f4f2f57e000-7f4f2f583000 rw-p 00000000 00:00 0
7f4f2f583000-7f4f2f59a000 r-xp 00000000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f4f2f59a000-7f4f2f799000 —p 00017000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f4f2f799000-7f4f2f79a000 r–p 00016000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f4f2f79a000-7f4f2f79b000 rw-p 00017000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f4f2f79b000-7f4f2f79f000 rw-p 00000000 00:00 0
7f4f2f79f000-7f4f2f7b4000 r-xp 00000000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f4f2f7b4000-7f4f2f9b3000 —p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f4f2f9b3000-7f4f2f9b4000 r–p 00014000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f4f2f9b4000-7f4f2f9b5000 rw-p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f4f2f9b5000-7f4f2f9da000 r-xp 00000000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f4f2f9da000-7f4f2fbd9000 —p 00025000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f4f2fbd9000-7f4f2fbda000 r–p 00024000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f4f2fbda000-7f4f2fbdb000 rw-p 00025000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f4f2fbdb000-7f4f2fcdc000 r-xp 00000000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f4f2fcdc000-7f4f2fedb000 —p 00101000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f4f2fedb000-7f4f2fedc000 r–p 00100000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f4f2fedc000-7f4f2fedd000 rw-p 00101000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f4f2fedd000-7f4f2ffc6000 r-xp 00000000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f4f2ffc6000-7f4f301c5000 —p 000e9000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f4f301c5000-7f4f301cd000 r–p 000e8000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f4f301cd000-7f4f301cf000 rw-p 000f0000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f4f301cf000-7f4f301e4000 rw-p 00000000 00:00 0
7f4f301e4000-7f4f30e2d000 r-xp 00000000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f4f30e2d000-7f4f3102d000 —p 00c49000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f4f3102d000-7f4f3103e000 r–p 00c49000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f4f3103e000-7f4f3105e000 rw-p 00c5a000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f4f3105e000-7f4f31060000 rw-p 00000000 00:00 0
7f4f31060000-7f4f31082000 r-xp 00000000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f4f31262000-7f4f3126a000 rw-p 00000000 00:00 0
7f4f3127d000-7f4f31281000 rw-p 00000000 00:00 0
7f4f31281000-7f4f31282000 r–p 00021000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f4f31282000-7f4f31283000 rw-p 00022000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f4f31283000-7f4f31284000 rw-p 00000000 00:00 0
7fff2c2fd000-7fff2c31e000 rw-p 00000000 00:00 0 [stack]
7fff2c37c000-7fff2c37e000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

How can i solve this problem? I would be very appreciated if you could give me some advice.

2

Hi,
I guess that you select just one group.
In that case, can you try a more recent version?
In alternative you can provide a link to the files
Best regards
Alessandra

3

Hi!
Thanks for reply. There are about 4000 bonds in my bonds.ndx file and they are divided into 2 groups. I choose one group a time to obtain the bonds length distribution.

I try to use gromacs2021.2 but it doesn’t work, the error information is the same.

4

Hi！
After I replace the Windows newline character in the bonds.ndx file with the Linux newline character, and divide the 4000 bonds into : Group 0 “bonds_core1” (3200 atoms), Group 1 “bonds_core2” (3200 atoms), Group 2 “bonds_term” (1600 atoms), then choose one group compute the bond length. Although there still exists en error, i can get the average bond length and xvg file. Here is the new bonds.ndx.

The new error:
GROMACS: gmx distance, version 2018.8
Executable: /sob/gmx2018.8/bin/gmx
Data prefix: /sob/gmx2018.8
Working dir: /mnt/hgfs/P2VP
Command line:
gmx distance -f NPT_cg.xtc -len 0.35 -tol 0.8 -n bonds.ndx -oh bonds-core1.xvg -select 0

Reading frame 17000 time 39000.000
Analyzed 17501 frames, last time 40000.000
bonds_core1:
Number of samples: 21001200
Average distance: 0.23086 nm
Standard deviation: 0.02758 nm

GROMACS reminds you: “What They Need’s a Damn Good Whacking” (The Beatles)

*** Error in `gmx’: double free or corruption (!prev): 0x000000000081ddb0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7fdf05b11489]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN13gmx_ana_pos_tD1Ev+0x1f)[0x7fdf0713a49f]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx8internal13SelectionDataD2Ev+0x34)[0x7fdf0713f0f4]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx19SelectionCollection4ImplD1Ev+0x89)[0x7fdf07141059]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx19SelectionCollectionD1Ev+0x19)[0x7fdf07141af9]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(+0x6aab78)[0x7fdf07168b78]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(+0x15189d)[0x7fdf06c0f89d]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZNSt8_Rb_treeISsSt4pairIKSsSt10unique_ptrIN3gmx18ICommandLineModuleESt14default_deleteIS4_EEESt10_Select1stIS8_ESt4lessISsESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E+0x4a)[0x7fdf06c0dfba]
/sob/gmx2018.8/bin/…/lib64/libgromacs.so.3(_ZN3gmx24CommandLineModuleManagerD1Ev+0x246)[0x7fdf06c0b236]
gmx[0x40dd6d]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fdf05ab23d5]
gmx[0x40de16]
======= Memory map: ========
00400000-00438000 r-xp 00000000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00637000-00638000 r–p 00037000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00638000-00639000 rw-p 00038000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00639000-0063a000 rw-p 00000000 00:00 0
007cf000-0088c000 rw-p 00000000 00:00 0 [heap]
7fdf00000000-7fdf00021000 rw-p 00000000 00:00 0
7fdf00021000-7fdf04000000 —p 00000000 00:00 0
7fdf05274000-7fdf05473000 r-xp 00000000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7fdf05473000-7fdf05672000 —p 001ff000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7fdf05672000-7fdf05683000 r–p 001fe000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7fdf05683000-7fdf05684000 rw-p 0020f000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7fdf05684000-7fdf0568b000 r-xp 00000000 fd:00 33674031 /usr/lib64/librt-2.17.so
7fdf0568b000-7fdf0588a000 —p 00007000 fd:00 33674031 /usr/lib64/librt-2.17.so
7fdf0588a000-7fdf0588b000 r–p 00006000 fd:00 33674031 /usr/lib64/librt-2.17.so
7fdf0588b000-7fdf0588c000 rw-p 00007000 fd:00 33674031 /usr/lib64/librt-2.17.so
7fdf0588c000-7fdf0588e000 r-xp 00000000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7fdf0588e000-7fdf05a8e000 —p 00002000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7fdf05a8e000-7fdf05a8f000 r–p 00002000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7fdf05a8f000-7fdf05a90000 rw-p 00003000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7fdf05a90000-7fdf05c52000 r-xp 00000000 fd:00 33665201 /usr/lib64/libc-2.17.so
7fdf05c52000-7fdf05e52000 —p 001c2000 fd:00 33665201 /usr/lib64/libc-2.17.so
7fdf05e52000-7fdf05e56000 r–p 001c2000 fd:00 33665201 /usr/lib64/libc-2.17.so
7fdf05e56000-7fdf05e58000 rw-p 001c6000 fd:00 33665201 /usr/lib64/libc-2.17.so
7fdf05e58000-7fdf05e5d000 rw-p 00000000 00:00 0
7fdf05e5d000-7fdf05e74000 r-xp 00000000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7fdf05e74000-7fdf06073000 —p 00017000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7fdf06073000-7fdf06074000 r–p 00016000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7fdf06074000-7fdf06075000 rw-p 00017000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7fdf06075000-7fdf06079000 rw-p 00000000 00:00 0
7fdf06079000-7fdf0608e000 r-xp 00000000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fdf0608e000-7fdf0628d000 —p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fdf0628d000-7fdf0628e000 r–p 00014000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fdf0628e000-7fdf0628f000 rw-p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fdf0628f000-7fdf062b4000 r-xp 00000000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7fdf062b4000-7fdf064b3000 —p 00025000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7fdf064b3000-7fdf064b4000 r–p 00024000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7fdf064b4000-7fdf064b5000 rw-p 00025000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7fdf064b5000-7fdf065b6000 r-xp 00000000 fd:00 33665209 /usr/lib64/libm-2.17.so
7fdf065b6000-7fdf067b5000 —p 00101000 fd:00 33665209 /usr/lib64/libm-2.17.so
7fdf067b5000-7fdf067b6000 r–p 00100000 fd:00 33665209 /usr/lib64/libm-2.17.so
7fdf067b6000-7fdf067b7000 rw-p 00101000 fd:00 33665209 /usr/lib64/libm-2.17.so
7fdf067b7000-7fdf068a0000 r-xp 00000000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7fdf068a0000-7fdf06a9f000 —p 000e9000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7fdf06a9f000-7fdf06aa7000 r–p 000e8000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7fdf06aa7000-7fdf06aa9000 rw-p 000f0000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7fdf06aa9000-7fdf06abe000 rw-p 00000000 00:00 0
7fdf06abe000-7fdf07707000 r-xp 00000000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7fdf07707000-7fdf07907000 —p 00c49000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7fdf07907000-7fdf07918000 r–p 00c49000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7fdf07918000-7fdf07938000 rw-p 00c5a000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7fdf07938000-7fdf0793a000 rw-p 00000000 00:00 0
7fdf0793a000-7fdf0795c000 r-xp 00000000 fd:00 33665194 /usr/lib64/ld-2.17.so
7fdf07b3c000-7fdf07b44000 rw-p 00000000 00:00 0
7fdf07b58000-7fdf07b5b000 rw-p 00000000 00:00 0
7fdf07b5b000-7fdf07b5c000 r–p 00021000 fd:00 33665194 /usr/lib64/ld-2.17.so
7fdf07b5c000-7fdf07b5d000 rw-p 00022000 fd:00 33665194 /usr/lib64/ld-2.17.so
7fdf07b5d000-7fdf07b5e000 rw-p 00000000 00:00 0
7ffe47225000-7ffe47246000 rw-p 00000000 00:00 0 [stack]
7ffe47276000-7ffe47278000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

5

Hi,
It seems a bug to me. Can you file it on GROMACS gitlab, including all the input file?
Thank you
Alessandra

6

I’m very grateful for your help.This is the link: Problem about ‘gmx distance’, realloc(): invalid next size (#4085) · Issues · GROMACS / GROMACS · GitLab
Thank you!