Solvate non-water molecule in a box, binary solvent

User discussions
1

GROMACS version: 2018
GROMACS modification: Yes/No
Hello
I ‘m using gromacs to simulate asphaltene aggregation in the presence of different solvents (it is an petroleum engineering major, to be clear).
Now, my aim is to build an initial configuration which contains this components:
20 molecules of asphaltene,
3000 molecules of toluene (solvent 1) and
finally fill the box with heptane (solvent 2) (no matter how many will be)
and size of the box will be: 121212

first I used gmx insert-molecules to build a box with 20 molecules of asphaltene in it.
For adding solvent 2, again, I used gmx insert-molecules and secesfuly did it.

But for the last step, I used gmx solvate to add solvent 3 but it didn’t go well. Instead of filling the box, limited number of solvent 2 was add.
(in this part, once I tested water molecules as 2nd solvent, the box was filled with it, I don’t now why)

Any help will be appreciated.
Thanks in advance

2

Copy and paste of command used and output would be a good idea.

3

Use Packmol, It will be much easier and better control to add different molecules in a box randomly. But first, check the actual density to calculate the total number of molecules required.

1 Like
4

Hi,

  1. building an initial box with 20 asphaltene molecules:
    gmx insert-molecules -ci asp.gro -box 12 12 12 -nmol 20 -o asp20.gro

  2. add 3000 toluene molecules to the box:
    gmx insert-molecules -f asp20.gro -ci tolu.gro -nmol 3000 -o asp20_tolu3000.gro

  3. fill the box with heptane molecule:
    gmx solvate -cp asp20_tolu3000.gro -cs hep.gro -o asp20_tolu3000_heptane.gro
    => results:
    Generating solvent configuration
    Will generate new solvent configuration of 5x5x5 boxes
    Solvent box contains 2875 atoms in 125 residues
    Removed 0 solvent atoms due to solvent-solvent overlap
    Removed 2231 solvent atoms due to solute-solvent overlap
    Sorting configuration
    Found 1 molecule type:
    hep ( 23 atoms): 28 residues
    Generated solvent containing 644 atoms in 28 residues
    Writing generated configuration to asp20_tolu3000_heptane.gro

Output configuration contains 47584 atoms in 3048 residues
Volume : 1728 (nm^3)
Density : 281.561 (g/l)
Number of SOL molecules: 0

4.fill the box with water (to better comparison ):
gmx solvate -cp asp20_tolu3000.gro -cs spc216.gro -o asp20_tolu3000_water.gro
=> results:
Generating solvent configuration
Will generate new solvent configuration of 7x7x7 boxes
Solvent box contains 186591 atoms in 62197 residues
Removed 16845 solvent atoms due to solvent-solvent overlap
Removed 54108 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 38546 residues
Generated solvent containing 115638 atoms in 38546 residues
Writing generated configuration to asp20_tolu3000_water.gro

Output configuration contains 162578 atoms in 41566 residues
Volume : 1728 (nm^3)
Density : 946.176 (g/l)
Number of SOL molecules: 38546

The point is gromacs recognize water molecules as a solvent But for heptane thats seems to be different.