H-bond calculation

User discussions
1

GROMACS version:2020.2
GROMACS modification: No
I am calculating the number of H-bond and ACF of H-bond using gmx hbond command. I have a bilayer which I have divided into bins along the z axis as: Interface region, Hydrophobic core and Far interface region. In each bin I am calculating h-bond between two groups which I have filtered using gmx select command and created their indices. This index I have used as input. I am using the following command:
hbond -f …/production.xtc -s …/production.tpr -n FR1_DMS_water.ndx -ac FR1.xvg -b 0 -e 50
but the error displays:Fatal error:
Partial overlap between groups ‘resname’ and ‘resname’

How can I resolve this??

2

There is no overlap between two molecules. I crosschecked the .gro file. Also the elements are differently named. Please help me understanding the error.

3

Please define different groups in your index file (*.ndx) and make sure you’re using the latest GROMACS version, 2023.2. Here is a discussion that might be helpful to you:

4

This is the index file.
[IW]
15241
15242
15243
15261
15262
15263
15525
15526
15527
15657
15658
15659
16001
16002
16003
16049
16050
16051
16229
16230
16231
16385
16386
16387
…[IDMS]
15473
15474
15475
16233
16234
16235
16309
16310
16311
16313
16314
16315
16613
16614
16615
16797
16798
16799
17177
17178
17179
17181
17182
~/Downloads/gromacs-2020.2/build_new/bin/gmx hbond -f …/…/production_500ps.xtc -s …/…/production_500ps.tpr -ac hbond_idms.xvg -b 450 -e 500 -n try.ndx
:-) GROMACS - gmx hbond, 2020.2 (-:

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GROMACS: gmx hbond, version 2020.2
Executable: /home/user/Downloads/gromacs-2020.2/build_new/bin/gmx
Data prefix: /home/user/Downloads/gromacs-2020.2 (source tree)
Working dir: /DATA2/DMSO+DMPC/simulation/Slipid/25%/gromacs-2020.2/new_pack/npt/production/production_500ps/h-bonds/generation_of_IW_IDMSO
Command line:
gmx hbond -f …/…/production_500ps.xtc -s …/…/production_500ps.tpr -ac hbond_idms.xvg -b 450 -e 500 -n try.ndx

Reading file …/…/production_500ps.tpr, VERSION 2020.2 (single precision)
Specify 2 groups to analyze:
Group 0 ( IW) has 393 elements
Group 1 ( IDMS) has 60 elements
Select a group: 1
Selected 1: ‘IDMS’
Select a group: 0
Selected 0: ‘IW’
Checking for overlap in atoms between IDMS and IW

Program: gmx hbond, version 2020.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2736)

Fatal error:
Partial overlap between groups ‘IDMS’ and ‘IW’

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation