How to run MD simulations

How to run MD simulation?

I. Preparation of softwares(Linux):

Moltemplate

Install Moltemplate: [https://www.moltemplate.org/download.html]

Comments: easy process in linux. git clone https://github.com/jewettaij/moltemplate moltemplate

Packmol

Install packmol: [http://leandro.iqm.unicamp.br/m3g/packmol/download.shtml]

Comments: Fill your email and then download

Lammps

Install Lammps: [https://lammps.sandia.gov/download.html]

Comments: The simplest way is to use cmake, which can be installed from https://cmake.org/install/

cd lammps                # change to the LAMMPS distribution directory
mkdir build; cd build    # create and use a build directory
cmake ../cmake           # configuration reading CMake scripts from ../cmake
cmake --build .          # compilation (or type "make")

II. Simulation

Following the first example https://www.moltemplate.org/examples.html

Download all files then:

moltemplate.sh system.lt

lmp_mpi -i run.in.npt

Tianhang Zhou

How to run MD simulations