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README.md

Generating a LAMMPS topology of a box of liquid water with pdb2lmp

In this tutorial we use packmol and pdb2lmp to generate a topology of a box of liquid water to be read in LAMMPS with the read_data command.

The files necessary to complete this tutorial (as well as the output files) are present in this directory.

Creating a box of liquid water with packmol

We start creating a with a 1000 molecules of water in the liquid phase. To find out the volume occupied by a single molecule of water, we calculate the molar volume Vm = molar weight / density of water and divide by the Avogadro number. Considering a cubic volume, we can get the side of a box of that volume:

Å

with being the water density (in kg/m3). If we consider 1000 kg/m3, we get L = 3.10432 Å, and if we consider that we want 1000 molecules in the box, we must multiply L by 10001/3, obtaining that our box must have a 31.0432 Å side.

This information is provided in the packmol.inp file, in the inside box command. Read the commentaries in the packmol.inp file to understand how the box is created. Basically, packmol will use the configuration in the file water.pdb to create a box placing 1000 of these configurations randomly. You can run packmol with:

packmol < packmol.inp > packmol.out

A box.pdb file will be created. You can visualize the box with your preferred software (VMD, Jmol, etc).

Generating the topology from the PDB

With the box.pdb file you can generate the topology with pdb2lmp. To have a topology containing the correct atomic charges for the SPC/E water model, there is a spce_charges.txt file containing the atomic charges for the oxygen and hydrogen atoms within this model.

Run the command below and analyze the output file (topo.lmp):

python /path/to/pdb2lmp.py box.pdb --ignore-dihedrals --box-size 31.0432 31.0432 31.0432 --charges spce_charges.txt > topo.lmp

The --ignore-dihedrals option is used so the topology does not contain any information about dihedrals at all (as this water model has just 3 sites).

By running pdb2lmp as above, the script will use the provided box size box size. If you'd rather provide the box dimensions in your .pdb file, you can add the CRYST1 line to the PDB file. This is shown in the mod_box.pdb file. Using the CRYST1 is necessary if your box is not orthogonal.