# Fatal error: The solvent group SOL is not continuous

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-the-solvent-group-sol-is-not-continuous/7601>\
**Category:** User discussions\
**Created:** [November 10, 2023, 2:38am UTC](https://gromacs.bioexcel.eu/t/fatal-error-the-solvent-group-sol-is-not-continuous/7601 "2023-11-10T02:38:25Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![yenn](https://avatars.discourse-cdn.com/v4/letter/y/c37758/32.png) [@yenn](https://gromacs.bioexcel.eu/u/yenn)\
**Post date:** [November 10, 2023, 2:38am UTC](https://gromacs.bioexcel.eu/t/fatal-error-the-solvent-group-sol-is-not-continuous/7601/1 "2023-11-10T02:38:25Z")

</div>

GROMACS version:2020.4  
GROMACS modification: No

I pull off protein for umbrella sampling in gromacs.

While pulling, I need pull.xtc and pull.gro at specific time line. So I cut the pull.xtc and get conf files at 1 second intervals.  
I expect it would take too long time to calculate, so I modified the box size of the conf file with the command editconf.  
After correcting the box size, I tried to put solvation and ion in the specific timeline conf.gro file again and repeat the same calculation, but I keep getting errors.

```auto
when i type

>gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1

Fatal error:
The solvent group SOL is not continuous: index[893883]=900933,
index[893884]=902638

comes out

Here is my topology file...

[molecules]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
SOL 297961
NA 834
CL 870
SOL 1

```

i have read similar questions but i don’t know exact way to modify my topology file.

[The solvent group SOL is not continuous - User discussions - GROMACS forums (bioexcel.eu)](https://gromacs.bioexcel.eu/t/the-solvent-group-sol-is-not-continuous/962)

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<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 10, 2023, 10:11am UTC](https://gromacs.bioexcel.eu/t/fatal-error-the-solvent-group-sol-is-not-continuous/7601/2 "2023-11-10T10:11:33Z")

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As it says in the message, there should be one continuous block of solvent. You will need to modify your `topol.top` and `conf.gro` files. The topology file is easiest. It should be:

```auto
[molecules]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
SOL 297962
NA 834
CL 870

```

Regarding the gro file you will have to modify it by hand using a text editor. You will need to cut-and-paste the last three (assuming a three-site water model) coordinate lines in the file (keep in mind that the last line is the shape of the periodic box) and insert them at the end of the large block of solvent, approximately 1700 lines from the bottom. It does not matter that the atom numbers are no longer in the right order.

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<div class="post-metadata">

**Author:** ![yenn](https://avatars.discourse-cdn.com/v4/letter/y/c37758/32.png) [@yenn](https://gromacs.bioexcel.eu/u/yenn)\
**Post date:** [November 13, 2023, 12:37am UTC](https://gromacs.bioexcel.eu/t/fatal-error-the-solvent-group-sol-is-not-continuous/7601/3 "2023-11-13T00:37:58Z")

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At first, thank you for your careful and super kind reply.  
By your advice I edited my topology fie as

```auto
[molecules]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
SOL 297962
NA 834
CL 870

```

and

edited my gro file to

```auto
.. blahblah
   29CL CL 2622 0.514 5.891 25.849
   30CL CL 2623 14.543 11.947 23.290
   31CL CL 2624 12.403 13.849 24.292
   32CL CL 2625 2.401 11.369 29.275
   33CL CL 2626 10.275 10.404 33.752
   34CL CL 2627 14.172 10.858 12.741
   35CL CL 2628 11.105 9.463 12.681
   36CL CL 2629 1.795 11.257 19.147
   37CL CL 2630 12.263 9.565 16.099
   38CL CL 2631 11.095 12.842 24.497
   39CL CL 2632 16.095 11.693 19.005
   40CL CL 2633 0.127 9.666 31.835
   41CL CL 2634 15.598 12.719 39.034
   42CL CL 2635 15.052 0.390 22.804
   43CL CL 2636 0.967 11.627 30.566
   44CL CL 2637 2.079 0.932 34.372
   SOL 297962
   NA 834
   CL 870
   16.10986 14.09414 39.67946

```

and it still doesn’t work at all.  
I think \< 16.10986 14.09414 39.67946 \>  
is box size, so i think i paste the last three line in the right place.

but the same error comes out…  
\*\*  
Fatal error:  
The solvent group SOL is not continuous: index[893883]=900933,  
index[893884]=902638  
\*\*  
can you tell me what i am doing wrong right now?  
Thank you for your helpful support.

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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:** [November 13, 2023, 2:40am UTC](https://gromacs.bioexcel.eu/t/fatal-error-the-solvent-group-sol-is-not-continuous/7601/4 "2023-11-13T02:40:48Z")

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You have not properly edited the `.gro` file. All you need to do is move the last three SOL lines up so they immediately follow the end of the previous block. Do not copy topology information into the coordinate file; that is syntactically incorrect and will raise other errors.

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<div class="post-metadata">

**Author:** ![yenn](https://avatars.discourse-cdn.com/v4/letter/y/c37758/32.png) [@yenn](https://gromacs.bioexcel.eu/u/yenn)\
**Post date:** [November 15, 2023, 2:11pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-the-solvent-group-sol-is-not-continuous/7601/5 "2023-11-15T14:11:34Z")

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Thank you for amazing answer!!  
My work goes well by your advice!!  
Really appreciate for your help.