# Constant ph molecular dynamics using GROMACS FMM & Constant pH

**URL:** <https://gromacs.bioexcel.eu/t/constant-ph-molecular-dynamics-using-gromacs-fmm-constant-ph/11055>\
**Category:** User discussions\
**Created:** [January 16, 2025, 4:55pm UTC](https://gromacs.bioexcel.eu/t/constant-ph-molecular-dynamics-using-gromacs-fmm-constant-ph/11055 "2025-01-16T16:55:28Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![dulal](https://avatars.discourse-cdn.com/v4/letter/d/fbc32d/32.png) [@dulal](https://gromacs.bioexcel.eu/u/dulal)\
**Post date:** [January 16, 2025, 4:55pm UTC](https://gromacs.bioexcel.eu/t/constant-ph-molecular-dynamics-using-gromacs-fmm-constant-ph/11055/1 "2025-01-16T16:55:28Z")

</div>

GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
Dear Experts,

I install the gromacs that suppor the constant ph MD.

> **[GROMACS FMM/CpH](https://grubmueller.pages.mpcdf.de/docs-gromacs-fmm-constantph/)**
>
> Documentation and tutorials for the GROMACS FMM & Constant pH Codes

Then I do the following steps.

1. gmx pdb2gmx -o prot.gro -ignh -ff charmm36m-lambdadyn -water tip3p -ldglu -ldhis -ldasp -ldtyr -ldlys -f output.gro

2. gmx editconf -f prot.gro -o box.gro -box 30 30 30 -c -bt cubic

3. gmx solvate -cs spc216.gro -cp box.gro -p topol.top -o solv.gro

4. sed ‘s/HOH/SOL/g’ solv.gro \> SOLV.gro

5. gmx grompp -f genion.mdp -c SOLV.gro -o genion.tpr -p topol.top -maxwarn 1

6. gmx genion -s genion.tpr -o solvions.gro -p topol.top -pname SOD -nname CLA -conc 0.15 -neutral -cphcoupled -rminprotld 2.0 -rminld 3.0 -rtolld 0.3 -nobackup

But In the step 6th I got the following error message.

umber of (3-atomic) solvent molecules: 877739

Processing topology  
Replacing 4920 solute molecules in topology file (topol.top) by 2439 SOD and 2481 CLA ions, and 72 lambda dynamics counterions.  
Using random seed -1082671106.  
Lambda dyn counterion: Determining solvent molecules not too close to non solvent…  
For the solvent search, min. dist to non-solvent: 2.00, distance to residue 2.70 - 3.30 (tolerance included)  
877600 of 877739  
Found 867438 suitable solvents  
Lambda dyn counterion: Determining solvent molecules suitable for each residue…

The following protonable residues have 0 suitable water for counterion/buffer placement: 2 19 31 32 38 39 58

* * *

Program: gmx genion, version 2024-dev-20241209-eba91f0-unknown  
Source file: src/gromacs/gmxpreprocess/genion.cpp (line 321)

Fatal error:  
Some residue have no suitable solvent for buffer/counterion placement. Maybe  
try a bigger box?

## For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)