Name | Last modified | Size | Description | |
---|---|---|---|---|
Parent Directory | - | |||
Ar_rho=0.0333_fcc_unwrapped.xyz | 2013-01-31 10:48 | 36K | ||
Practical04PythonAndNumpy.pdf | 2013-02-10 21:08 | 100K | ||
PythonAndNumpy/ | 2013-02-10 21:06 | - | ||
assignment_07.txt | 2013-01-31 18:33 | 8.7K | ||
mdIO_v0.py | 2013-01-31 10:53 | 1.8K | ||
mdIO_v1.py | 2013-01-31 15:01 | 1.9K | ||
p04_class.txt | 2013-02-10 21:08 | 6.5K | ||
xyz/ | 2013-01-31 17:42 | - | ||
The XYZ file format is a very simple format to store positions of particles. It is described in VMD's XYZ Plugin. Basically, a XYZ file looks like this, with our own enhancement, the box dimensions
N box Lx Ly Lz title text atom1 x y z atom2 x y z ... atomN x y z
The first line is the number of atoms. The second a string. The string shoul;d start with the word box and then follow three float numbers that are the lengths of the orthorhombix unit cell. From the third line onwards, each line contains a symbol for the particle ("atomX") and the cartesian coordinates. All entries are white-space separated.
VMD is a versatile molecular visualization program. It is very good at displaying MD trajectories and is geared towards biopolymers and liquids but it can be used for a wide range of systems.
On the Macs, you will find it in /Applications.