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GROMACS solvation and adding ions (version 2022+galaxy0)

GRO structure file:

Topology (TOP) file:

Water model for solvation:

Note SPC is a generic equilibrated 3-point solvent model and can be used as the solvent configuration for any of SPC, SPC/E, or TIP3P water.

Add ions to neutralise system?:

If system is charged, replace an appropriate number of randomly selected solvent molecules with sodium or chloride ions to neutralise it.

Specify salt concentration (sodium chloride) to add, in mol/liter:

Note existing ions in the system are not taken into account - including those added if the neutralise option is selected. Ions are added by randomly replacing water molecules.

Random seed for adding ions:

Select a random seed for replacing solvent with ions. Set to 0 to generate a seed.

Maximum warnings to allow.:

Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail.

Generate detailed log:

Generate detailed log information that can be summarized with ParseLog.

What it does

This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions can be added if necessary to ensure the system is charge-neutral.

Input

GRO structure file.

Topology (TOP) file.

In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup.

Output

GRO structure file.