--- moltemplate specific ---
If you want to change the force field, you will have to edit the "ch2group.lt
", and "alkane50.lt
" files to replace the "inherits OPLSAA", with "inherits MYFORCEFIELD" and you will have to create a file containing the contents of the "MYFORCEFIELD" object and edit the "ch2group.lt
" and "ch3group.lt
" files to change the names of the @atom types accordingly.
You can control the size of the simulation box by editing the "system.lt
" file. You can also do this later on by editing the header portion at the top of the "system.data" file generated by moltemplate.
If you want to have multiple chains, you can follow the "hexadecane" example, "examples" directory distributed with moltemplate (available using both the OPLSAA and AMBER force fields). You control the spacing between molecules by editing the .move() commands, and changing the "Data Boundary" section of the "system.lt
If you want to create a large polymer melt instead of a few short polymers, then you can generate the initial backbone coordinates using the "ndmansfield" utility, and "wrap" your polymer along the direction of the curve either by writing your own script (with a simple for-loop to generate part of the text file which moltemplate reads), or by using the "genpoly_lt.py" utility which is distributed with moltemplate, and is documented here: