How to determine the amount of solvent added to the simulation box?

User discussions
1

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,
Thank you.

2

Hi,
gmx solvate has an option to control the max number of solvent molecules ( -maxsol) . But not sure that solve your issue.
Maybe an alternative is to look at A (or/and B) concentrations in water (if the experiments are performed at constant concentration of A and/or B in water,) in place of the number of water.
\Alessandra

3

I see, thank you for your enlightenment, Mrs. Alessandra.
I will try it first.

4

Hi @ayyaxyz ,
Could you please tell me how did you get/create the tip4p_2005.gro file?

Thanks