# Non-water solvation

**URL:** <https://gromacs.bioexcel.eu/t/non-water-solvation/9328>\
**Category:** User discussions\
**Tags:** simulation-setup\
**Created:** [June 6, 2024, 4:32pm UTC](https://gromacs.bioexcel.eu/t/non-water-solvation/9328 "2024-06-06T16:32:04Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![js\_gro](https://avatars.discourse-cdn.com/v4/letter/j/ac8455/32.png) [@js\_gro](https://gromacs.bioexcel.eu/u/js_gro)\
**Post date:** [June 6, 2024, 4:32pm UTC](https://gromacs.bioexcel.eu/t/non-water-solvation/9328/1 "2024-06-06T16:32:04Z")

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GROMACS version: gromacs/2023  
GROMACS modification: No  
Here post your question

Can you assist with the simulation workflow for solvating with a non-water solvent and provide the compressibility values needed for methanol and THF?

Currently:

1. gmx pdb2gmx --ff oplsaa -f methanol.pdb -water none -o methanol.gro -p topol\_solvent.top

2. gmx insert-molecules -ci methanol.gro -nmol 4000 -box 5 5 5 -o solvent.gro

3. gmx grompp -f minim.mdp -c solvent.gro -p topol\_solvent.top -o minim.tpr  
gmx mdrun -s minim.tpr -deffnm min

4. gmx grompp -f NVT\_Equilibration.mdp -c min.gro -p topol\_solvent.top -o nvt.tpr  
gmx mdrun -s nvt.tpr -deffnm nvt

5. gmx grompp -f NPT\_Equilibration.mdp -c nvt.gro -r nvt.gro -p topol\_solvent.top -o npt.tpr  
gmx mdrun -s npt.tpr -deffnm npt

6. gmx pdb2gmx --ff oplsaa -f 2\_10\_chains\_$1\_sulf\_$2.pdb -water none -o structure.gro  
gmx editconf -f structure.gro -o system.gro -bt cubic -box 15 15 15

gmx solvate -cp system.gro -cs npt.gro -o system\_solvated.gro -p topol.top

Error in NPT equilibration step:  
Step 2226 Pressure scaling more than 1%. This may mean your system is not yet equilibrated. Use of Parrinello-Rahman pressure coupling during equilibration can lead to simulation instability, and is discouraged.

Error in solvation:  
Few methanol solvent outside the box