Build a solvent box in TINKER

The TINKER utility xyzedit has the ability to build solvent boxes. A molecular structure in TINKER format of the solvent molecules is required:

xyzedit -k ethylene.key

the following menu' is displayed:

he XYZ Coordinate Editing Facility can Provide :

    (1) Offset the Numbers of the Current Atoms
    (2) Deletion of Individual Specified Atoms
    (3) Deletion of Specified Types of Atoms
    (4) Deletion of Atoms outside Cutoff Range
    (5) Insertion of Individual Specified Atoms
    (6) Replace Old Atom Type with a New Type
    (7) Assign Connectivities based on Distance
    (8) Convert Units from Bohrs to Angstroms
    (9) Invert thru Origin to give Mirror Image
   (10) Translate All Atoms by an X,Y,Z-Vector
   (11) Translate Center of Mass to the Origin
   (12) Translate a Specified Atom to the Origin
   (13) Translate and Rotate to Inertial Frame
   (14) Move to Specified Rigid Body Coordinates
   (15) Move Stray Molecules into Periodic Box
   (16) Create and Fill a Periodic Boundary Box
   (17) Soak Current Molecule in Box of Solvent
   (18) Append a Second XYZ file to Current One

 Number of the Desired Choice [<CR>=Exit] :

The solvent box is created with the option 16. The program will ask you the number of molecules to put in the box and the size of the box along the direction X, Y and Z1. If you want to build a solvent box at a certain density, you can use the script
vol2mol to get the proper number of molecules.

A cubic solvent box of dimethyl ether is shown in the image below.


If you want to check how good your force field is to describe the liquid, you can try to equilibrate the box in NPT ensemble and see if you can match or maintain the correct (i.e., experimental) density. Otherwise you can work directly in NVT at the proper liquid density.
Once a solvent box is built, with the option 17 of xyzedit you can soak in it a molecular system, so to have a solute/solvent solution. Be careful that molecules of solvent are removed to make room for the solute and the density now could be lower than expected. A NPT equilibration could be required in order to change the volume of the system and have the right density again. Also, mind that, at least with TINKER 4.2, sometimes there are problems in the generated box for high density.

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