# How to identify or create correct list from GROMACS options during analysis of trajectory?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-identify-or-create-correct-list-from-gromacs-options-during-analysis-of-trajectory/1637>\
**Category:** User discussions\
**Created:** [February 24, 2021, 2:23pm UTC](https://gromacs.bioexcel.eu/t/how-to-identify-or-create-correct-list-from-gromacs-options-during-analysis-of-trajectory/1637 "2021-02-24T14:23:51Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Exon53](https://avatars.discourse-cdn.com/v4/letter/e/f475e1/32.png) [@Exon53](https://gromacs.bioexcel.eu/u/Exon53)\
**Post date:** [February 24, 2021, 2:23pm UTC](https://gromacs.bioexcel.eu/t/how-to-identify-or-create-correct-list-from-gromacs-options-during-analysis-of-trajectory/1637/1 "2021-02-24T14:23:51Z")

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GROMACS version: 2020.4  
GROMACS modification: No

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein\_chain\_A and Protein\_chain\_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list :

Group 0 ( System) has 180960 elements

Group 1 ( Protein) has 12511 elements

Group 2 ( Protein-H) has 6408 elements

Group 3 ( C-alpha) has 791 elements

Group 4 ( Backbone) has 2373 elements

Group 5 ( MainChain) has 3166 elements

Group 6 ( MainChain+Cb) has 3910 elements

Group 7 ( MainChain+H) has 3924 elements

Group 8 ( SideChain) has 8587 elements

Group 9 ( SideChain-H) has 3242 elements

Group 10 ( Prot-Masses) has 12511 elements

Group 11 ( non-Protein) has 168449 elements

Group 12 ( Ion) has 26 elements

Group 13 ( ZN) has 1 elements

Group 14 ( CL) has 1 elements

Group 15 ( NA) has 24 elements

Group 16 ( Water) has 168423 elements

Group 17 ( SOL) has 168423 elements

Group 18 ( non-Water) has 12537 elements

Group 19 ( Water\_and\_ions) has 168449 elements

There is no mention of Chains A and B. I would like to calculate H-bond between Chain A and Chain B and later do a SMD simulation between these two groups. However, I do not see them in the list.

How to fix this issue ?

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [February 24, 2021, 7:19pm UTC](https://gromacs.bioexcel.eu/t/how-to-identify-or-create-correct-list-from-gromacs-options-during-analysis-of-trajectory/1637/2 "2021-02-24T19:19:01Z")

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Use `make_ndx` to generate index groups corresponding to the different chains.

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<div class="post-metadata">

**Author:** ![Exon53](https://avatars.discourse-cdn.com/v4/letter/e/f475e1/32.png) [@Exon53](https://gromacs.bioexcel.eu/u/Exon53)\
**Post date:** [February 28, 2021, 12:16am UTC](https://gromacs.bioexcel.eu/t/how-to-identify-or-create-correct-list-from-gromacs-options-during-analysis-of-trajectory/1637/3 "2021-02-28T00:16:06Z")

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After using pdb2gmx on the cleaned PDB (only removed crystallographic waters), chain A has “resnr” from 19-615 and chain B has “resnr” from 333-526.

When I use make\_ndx, how will it differentiate , as the numbers 333-526 are included in the IDs for the first chain as well. The total number of atoms for group protein does not equal to the two groups when I use make\_ndx to create two separate groups by using “resnr”

As in the question group Protein has 12511 elements

This is what I observe upon using make\_ndx :

> r 19-615  
> Found 12511 atoms with res.nr. in range 19-615  
> 15 r\_19-615 : 12511 atoms  
> r 333-526  
> Found 6116 atoms with res.nr. in range 333-526  
> 16 r\_333-526 : 6116 atoms

[Link to GRO file](http://s000.tinyupload.com/index.php?file_id=00737274584277733802)