Hi
I am new to LAMMPS, and trying to learn how to simulate liquid molecular environments, I was looking for a way of generating input structure files, I've come across so many different software (such as vmd and its plugins which is not user friendly and was a waste of time), does anyone know any good tutorial to learn how to build such input file (if we don't use already available pdb files)? I am quite familiar with Gaussian, is there any way to get the structure of one molecule from the Gaussian and build the pdb file based on that? I understand that we probably need more than one molecule as the input molecular structure.
Hi
Misha Urazaliev Thanks I went through those commands and still not clear to me, will you please give an example input file for such molecular structure?
Above I meant structure file. That is the configuration of the molecules.
There are several types of input files.
For example:
1. Structure file
2. Potential interaction file
3. Molecular file.
http://www.isimuly.cn/lammps/molecule.html
If you are just starting to write a script, then it is better to get by with fewer input files. But in your case molecule input file is needed.
Please see how the examples look like:
~/lammps/examples/deposit
Inside are the script files and the file that defines the molecule:
molecule.dimer
http://www.isimuly.cn/lammps/create_atoms.html
https://matsci.org/t/generation-of-water-molecules-by-lammps/44342
https://matsci.org/t/how-to-create-a-new-molecule-during-simulation/31690
Misha Urazaliev Thanks for your answer, I guess my main question is how to generate such input molecule file, I know how it looks (containing atom types and their coordinate) but is that something we write manually or is there any package that generate it?
Tahereh Alavi, to answer your question, see here:
https://github.com/jewettaij/moltemplate/releases
http://moltemplate.org/
http://www.isimuly.cn/lammps/molecule.html
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