Creating a water box using lammps perl script

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1

Hi, could anybody suggest me in creating a water box only (no solute inside) with perl script of lammps of preferred dimension.

2

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):

http://moltemplate/blob/master/doc/moltemplate_manual_src/waterSPCEx1000_LR.jpg

Input files are located here:

http://moltemplate.org/examples/waterSPCE_simple/

It is explained in detail on pages 13-17 of the moltemplate manual located here:
http://moltemplate.org/doc/

More complicated examples to follow:

Here’s an example of SPC/E water mixed with sodium chloride ions:
http://moltemplate.org/images/waterSPCE+Na+Cl/waterSPCE+Na+Cl_t=0.jpg

Input files here:
http://moltemplate.org/examples/waterSPCE+Na+Cl/

Here is a more complex example including a carbon nanotube and water:

http://moltemplate.org/visual_examples.html#nanotube+water

(Click below each image for the corresponding input file.)

Here is an example of water mixed with methane using the OPLSAA force field:

https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/waterSPCE%2Bmethane

Here is an example of water mixed with another small molecule (isobutane) using the Amber GAFF force field:

https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_AMBER/waterTIP3P%2Bisobutane

Here are some non-moltemplate options:

topotools:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial—part-2

a perl script from Laurent Joly:
http://lammps.sandia.gov/user/script9/cnt.pl

Picture here:
http://lammps.sandia.gov/user/script9/n30.jpg

Also see:

http://lammps.sandia.gov/prepost.html

and
https://sourceforge.net/projects/moleculardynami/

Cheers

-andrew

3

Thanks Andrew for valuable input.