There are plenty of Molecular Dynamics packages out there, but what is LAMMPS and why could or should you use it and how does it differ from say Amber or CHARMM? Here are some of the LAMMPS features that I have lifted from the front page of LAMMPS at http://lammps.sandia.gov/: LAMMPS is a classical molecular [...]
Calculating mean squared displacement for membranes
Often one wants to understand how best to determine the phase of a simulated lipid membrane. One way is to use the Mean Squared Displacement (MSD) method where one measures how far lipids move with respect to a centre of mass. This way its easy to determine whether your membrane is in a gel or [...]
How to find clusters from your molecular dynamics simulations
Given a series of molecules or atoms – how do we define clusters? Well there are a number of approaches that one can look at from all kinds of fields. One could even use machine learning to recognize clusters, however being a pragmatist, one finds the simple method is often the best, rather than spending [...]
Computing the dipole orientation of a cluster in VMD
One tool that has generic use beyond just membranes is the dipole viewer code for VMD. The TCL/TK script aims to analyse a cluster over a time range and determine the dipole orientation and properties such as orientation with respect to a lipid tail. You might find some of the code excerpts useful for understanding [...]
Building a lipid membrane from scratch
We wanted to be able to build multiple component lipid membrane systems for simulation with the Molecular Dynamic Framework called LAMMPS, so we set about building a series of routines cut in Python that would help us and anyone build systems – solvated or otherwise with relative ease. Of course, you will need to have [...]