# Assistance with “Scattered Bound Ion Issue” in GROMACS Trajectory Extraction

**URL:** <https://gromacs.bioexcel.eu/t/assistance-with-scattered-bound-ion-issue-in-gromacs-trajectory-extraction/11151>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [January 26, 2025, 8:19pm UTC](https://gromacs.bioexcel.eu/t/assistance-with-scattered-bound-ion-issue-in-gromacs-trajectory-extraction/11151 "2025-01-26T20:19:25Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mehdi60](https://avatars.discourse-cdn.com/v4/letter/m/a698b9/32.png) [@mehdi60](https://gromacs.bioexcel.eu/u/mehdi60)\
**Post date:** [January 26, 2025, 8:19pm UTC](https://gromacs.bioexcel.eu/t/assistance-with-scattered-bound-ion-issue-in-gromacs-trajectory-extraction/11151/1 "2025-01-26T20:19:25Z")

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GROMACS version: GROMACS\_2023.3 to run MD for a protein with charmm36-jul2022 force-field  
GROMACS modification: No

Dear GROMACS Experts, I have extracted a frame from trajectory files (xtc) of a protein that contains four bound ions: three calcium and one sodium ion. After using trjconv with the -pbc mol -center option to address periodicity, I found that while the protein is centered, the ions are scattered around it. I have tried several strategies to resolve this issue, including:  
1. Using -pbc whole -center  
2. Applying an index file for selecting the Protein+3Ca+1Na group (Group 20)  
3. Implementing rotational and translational fitting with -fit rot+trans  
4. Using -pbc cluster  
Despite these attempts, the ions remain misaligned. Could you please advise on the following:  
1. How can I correct the positioning of these ions?  
2. Is it acceptable to proceed with MD file preparation and subsequent analyses (e.g., RMSD, RMSF) using only the protein data without correcting the ion positions?  
3. If I extract a PDB of the frame without ions, can I manually add them later for molecular docking?  
Also I send you Groups related to MD run of protein and contains of files including “topol.top” and “topol\_Other.itp”:  
Group 0 ( System) has 69294 elements  
Group 1 ( Protein) has 6666 elements  
Group 2 ( Protein-H) has 3459 elements  
Group 3 ( C-alpha) has 425 elements  
Group 4 ( Backbone) has 1275 elements  
Group 5 ( MainChain) has 1699 elements  
Group 6 ( MainChain+Cb) has 2086 elements  
Group 7 ( MainChain+H) has 2112 elements  
Group 8 ( SideChain) has 4554 elements  
Group 9 ( SideChain-H) has 1760 elements  
Group 10 ( Prot-Masses) has 6666 elements  
Group 11 ( non-Protein) has 62628 elements  
Group 12 ( Other) has 3 elements  
Group 13 ( CAL) has 3 elements  
Group 14 ( NA) has 15 elements  
Group 15 ( Ion) has 15 elements  
Group 16 ( Water) has 62610 elements  
Group 17 ( SOL) has 62610 elements  
Group 18 ( non-Water) has 6684 elements  
Group 19 ( Water\_and\_ions) has 62625 elements  
Group 20 (Protein\_3CA\_1NA) has 6670 elements

“topol.top” contains: →  
; Include forcefield parameters  
#include “./charmm36-jul2022.ff/forcefield.itp”

; Include chain topologies  
#include “topol\_Protein\_chain\_B.itp”  
#include “topol\_Other.itp”

; Include water topology  
#include “./charmm36-jul2022.ff/tip3p.itp”

#ifdef POSRES\_WATER  
; Position restraint for each water oxygen  
[position\_restraints]  
; i funct fcx fcy fcz  
1 1 1000 1000 1000  
#endif

; Include topology for ions  
#include “./charmm36-jul2022.ff/ions.itp”

[system]  
; Name  
A1CC-425aa - homology model built on 4DOU\_A in water

[molecules]  
; Compound #mols  
Protein\_chain\_B 1  
Other 1  
SOL 20870  
NA 14

“topol\_Other.itp” contains: →  
[moleculetype]  
; Name nrexcl  
Other 3

[atoms]  
; nr type resnr residue atom cgnr charge mass typeB chargeB massB  
; residue 0 CAL rtp CAL q +2.0  
1 CAL 01 CAL CAL 1 2 40.08 ; qtot 2  
; residue 0 CAL rtp CAL q +2.0  
2 CAL 02 CAL CAL 2 2 40.08 ; qtot 4  
; residue 0 CAL rtp CAL q +2.0  
3 CAL 03 CAL CAL 3 2 40.08 ; qtot 6  
; residue 0 SOD rtp SOD q +1.0  
4 SOD 04 NA NA 4 1 22.9898 ; qtot 7

; Include Position restraint file  
#ifdef POSRES  
#include “posre\_Other.itp”  
#endif

Thank you for your guidance. Best regards

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<div class="post-metadata">

**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [January 27, 2025, 8:24am UTC](https://gromacs.bioexcel.eu/t/assistance-with-scattered-bound-ion-issue-in-gromacs-trajectory-extraction/11151/2 "2025-01-27T08:24:14Z")

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How do you know that the ions stayed bound during the simulation? Are you sure they just didn’t leave the starting positions where they were?