Hi, could anybody suggest me in creating a water box only (no solute inside) with perl script of lammps of preferred dimension.
I don’t know why it has to be a perl script. I’ll show some moltemplate examples followed by some other options (including a perl script)
First of all, here’s an example of a box of water using moltemplate (python, bash):
Input files are located here:
It is explained in detail on pages 13-17 of the moltemplate manual located here:
More complicated examples to follow:
Here’s an example of SPC/E water mixed with sodium chloride ions:
Input files here:
Here is a more complex example including a carbon nanotube and water:
(Click below each image for the corresponding input file.)
Here is an example of water mixed with methane using the OPLSAA force field:
Here is an example of water mixed with another small molecule (isobutane) using the Amber GAFF force field:
Here are some non-moltemplate options:
a perl script from Laurent Joly:
Thanks Andrew for valuable input.