Non-water solvation

User discussions
1

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