Combine the atoms of two different simulations in a new simulation box

Hi Christopher

There were a couple recent posts on this topic (see below).

I assume you have separate DATA files for each system you want to combine.

In addition to manually using a text-editor, as Ray suggested, there are several tools to merge multiple data files together:

  1. read_data (the lammps input-script command):
    http://sourceforge.net/p/lammps/mailman/message/34481431/

  2. pizza.py (a python module):
    http://lammps.sandia.gov/threads/msg11838.html

  3. topotools (included with VMD):
    https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial—various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal

  4. moltemplate.sh (a stand-alone program):

http://lammps.sandia.gov/threads/msg55306.html
http://sourceforge.net/p/lammps/mailman/message/34482391/
http://lammps.sandia.gov/threads/msg41643.html

Moltemplate allows you to turn each DATA file into a “molecule-object”. These objects include coordinates, charges, masses, bonds, angles, dihedrals, impropers, constraints, groups, and force-field information for each system. You can manually move and rotate these objects, duplicate them, and combine them together, and even delete individual atoms (to prevent atom overlap, for example). However moltemplate does not currently detect atom-overlap and remove solvent molecules automatically. (Topotool can.) If you decide to use moltemplate, be sure to download the latest version at www.moltemplate.org. (Incidentally, there were some relevant bugs fixed on 2015-9-22)
Cheers

Andrew

Thanks to everyone who provided answers to my question . I will evaluate the different options to choose one.

Personally I think that this issue should be on a wiki or how-to section , sure to be a recurring question .

Cheers

Thanks to everyone who provided answers to my question . I will evaluate
the different options to choose one.

Personally I think that this issue should be on a wiki or how-to section ,
sure to be a recurring question .

it is ​not as recurring as other​s. most people either create inputs from
scratch from within LAMMPS or have to have a tool to prepare their original
inputs. expanding that to generate a combined input is usually
straightforward. if i remember correctly, andrew's moltemplate tool started
this way.

there would be a wiki or faq, if we could only find some people that would
be willing to maintain it....

axel.