# Problem about 'gmx distance'

**URL:** <https://gromacs.bioexcel.eu/t/problem-about-gmx-distance/2391>\
**Category:** User discussions\
**Tags:** mdrun, analysis-tools\
**Created:** [June 21, 2021, 12:31pm UTC](https://gromacs.bioexcel.eu/t/problem-about-gmx-distance/2391 "2021-06-21T12:31:48Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![LEE](https://avatars.discourse-cdn.com/v4/letter/l/bc8723/32.png) [@LEE](https://gromacs.bioexcel.eu/u/LEE)\
**Post date:** [June 21, 2021, 12:31pm UTC](https://gromacs.bioexcel.eu/t/problem-about-gmx-distance/2391/1 "2021-06-21T12:31:49Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [June 22, 2021, 1:31pm UTC](https://gromacs.bioexcel.eu/t/problem-about-gmx-distance/2391/2 "2021-06-22T13:31:27Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![LEE](https://avatars.discourse-cdn.com/v4/letter/l/bc8723/32.png) [@LEE](https://gromacs.bioexcel.eu/u/LEE)\
**Post date:** [June 23, 2021, 12:54am UTC](https://gromacs.bioexcel.eu/t/problem-about-gmx-distance/2391/3 "2021-06-23T00:54:55Z")

</div>

Hi!  
Thanks for reply. There are about 4000 bonds in my [bonds.ndx](https://raw.sevencdn.com/HEU-F8-PRACTICE/stor/master/20210623/aa2cc2088128128174b6ad423af5e8b0/aa2cc2088128128174b6ad423af5e8b0.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.

---

<div class="post-metadata">

**Author:** ![LEE](https://avatars.discourse-cdn.com/v4/letter/l/bc8723/32.png) [@LEE](https://gromacs.bioexcel.eu/u/LEE)\
**Post date:** [June 23, 2021, 3:14am UTC](https://gromacs.bioexcel.eu/t/problem-about-gmx-distance/2391/4 "2021-06-23T03:14:27Z")

</div>

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](https://raw.sevencdn.com/HEU-F8-PRACTICE/stor/master/20210623/b2d890f64c1e33b0c00d84ca0f7c6cb4/b2d890f64c1e33b0c00d84ca0f7c6cb4.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)

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [June 24, 2021, 11:17am UTC](https://gromacs.bioexcel.eu/t/problem-about-gmx-distance/2391/5 "2021-06-24T11:17:55Z")

</div>

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

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<div class="post-metadata">

**Author:** ![LEE](https://avatars.discourse-cdn.com/v4/letter/l/bc8723/32.png) [@LEE](https://gromacs.bioexcel.eu/u/LEE)\
**Post date:** [June 25, 2021, 2:06am UTC](https://gromacs.bioexcel.eu/t/problem-about-gmx-distance/2391/6 "2021-06-25T02:06:29Z")

</div>

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