GROMACS version: 2021.4
GROMACS modification: No
I will do a simulation with various number of molecules A and B in TIP4P/2005 water as the solvent.
Here are the variations:
- Variation 1 = 25 molecules of A and 5 molecules of B
- Variation 2 = 25 molecules of A and 10 molecules of B
- Variation 3 = 25 molecules of A and 15 molecules of B
- Variation 4 = 5 molecules of A and 25 molecules of B
- Variation 5 = 10 molecules of A and 25 molecules of B
- Variation 6 = 15 molecules of A and 25 molecules of B
Variations in the number of molecules are arranged using Packmol with a maximum random coordinate of 60 Angstroms along the x, y, and z axis (0. 0. 0. 60. 60. 60.).
Then, I turned it into a simulation box with module
gmx editconf -f initial.pdb -o box.gro -bt cubic -d 1.0
Then, I added the water molecule TIP4P/2005 using the module
gmx solvate -cp box.gro -cs tip4p_2005.gro -p topol.top -o solv.gro
I want the simulation system to only be affected by the difference in the number of molecules so that it’s like an experiment in a laboratory where the system will be more concentrated with a constant amount of solvent.
However, a problem arises, namely the amount of water solvent added is different for each variation. The amount of water solvent increases with increasing molecular variation.
How to handle it?
How to set the amount of TIP4P/2005 water solvent added to the simulation box for different number of molecules variation?
Please help me,