MD+theory


 * ==Umbrella sampling==
 * ==Parallel simulation==
 * ==Compare Gromacs and Desmond==

Umbrella sampling
Umbrella sampling could be useful to obtain a PMF (and all it's derivatives) for systems where direct PMF calculation is time consuming (for example in the case of deep PMF minimum for the particular configuration). Very nice tutorial is represented at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html

Parallel simulation
If a system for example is sensitive to the initial parameters configuration, it is convenient to calculate a few systems in parallel. There are a few ways to create initial configuration: It is usually convenient to keep all files for one system in one folder, so that every system has its own folder. One could find a template for python script ([|template.py]) that takes care of starting every simulation (or performing analysis) from its own folder.
 * to assign different initial velocities for particles in the system (different random generator number);
 * to start with different initial configuration (ex. Packmol or produce a short trajectory at high temperature and take different frames)
 * to combine different velocities and initial coordinates.

Compare Gromacs and Desmond

 * =  ||= Gromacs (4.5.2) ||= Desmond (2.4) ||= comment ||
 * = speed of calculation(~10 000 particles) ||= on Halimede: 1.3 - 5 ns/day (10 CPU) ||= on Halimede: 8-15 ns/day (8 CPU) ||= depends on the network ||
 * = support of electrostatics for slab geometry ||= + ||= - ||=  ||
 * = documentation ||= a lot, but unstructured time to time ||= often insufficient, Desmond user group is rather slow ||=  ||
 * = analysis tools ||= well documented, big amount ||= poorly documented => hard to find the proper tool for 'THE' task ||=  ||
 * = trajectory size ||= 3X ||= X ||=  ||
 * = 'A' molecular topology ||= - ||= + ||= mind 'Convert.py' script by Kathleen ||
 * = maximum system size, particles ||= 99999 ||= - ||=  ||