Depending on the version of VMD, it may or may not "unwrap" the periodic boundaries if the particle moves through them. To view the dump file in VMD, choose "New Molecule" from the file menu, click browse to find the file, and select "LAMMPS Trajectory" from the drop down list before hitting "Load". LAMMPS keeps track of movement through the periodic boundaries. if the particle moves out of one the edge of the box, it appears on the other side of the box. In this simulation the particle is diffusing in a "periodic box", i.e. In LAMMPS we use the NVE and langevin fixes, which results in an NVT system ( canonical ensemble) LAMMPS uses a velocity-Verlet update rule. Where atoms experience random forces ( ) and viscous drag ( ) from an implied solvent. Here were are using LAMMPS to run a Langevin Dynamics simulation (sometimes called Brownian Dynamics), where the position of atoms are described by a Langevin equation vmd to visualize the simulation trajectory (see below). The output files include a "dump file" which contains the positions of the atom at regular time steps, and a "thermo file" which contains thermodynamic information at regular time steps. The configuration file cannot contain any comments, but the details of how to lay out this file are here in the LAMMPS manual. Look at the comments in the in.diffusing_particle file for details of each command. lmp_serial < diffusing_particle.lam Some messages will be printed to the screen, and some output files created. To run LAMMPS using these files, download them to a new directory where there is a copy of the LAMMPS executable and type. The input script and initial conditions files are diffusing_particle.lam and initial_configuration.txt. The way we will use LAMMPS requires two input files: a script which tells LAMMPS what to do, and an initial configuration file which gives the initial coordinates of each atom in the system, as well as other information.įor the first example we will simulate a single atom diffusing in an implicit solvent. For section 6 LAMMPS must be compiled with the ASPHERE packages and some additional custom interaction styles.Ģ. All the packages required to do the simulations in 2-5 below should be enabled by default (if you download via git checkout you might need to install them). Make serial or make mpi to compile serial or mpi versions. To compile with the basic packages, download and unpack, switch to the src/ directory and type: The LAMMPS source code can be downloaded as a tarball from the LAMMPS website: /download.html. The input scripts include further comments detailing what each command does. I've tried to add links to the LAMMPS manual and other sources where appropriate. This is a very simple and quick tutorial on how to use LAMMPS to simulate a polymer using Langevin dynamics.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |