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Analyzing simulations with LOOS
Other documents will cover issues specific to particular packages (e.g. NAMD, gromacs). The purpose of this document is to give you an idea how LOOS expects you to think about your data, and to clarify our notation and terminology. LOO
To figure out what tools are available, go to the main tool documentation. To learn more about how a particular tool works, run the command toolname --fullhelp; this will give you a discussion of the options, details about the algorithms, suggested workflows, and possible pitfalls, as well as references to the literature where appropriate. To just get a list of available options, you can just run the tool with no command line options.
This document assumes you've already built LOOS. If not, look at INSTALL.md in the top-level directory for instructions, including the commands you'll need to install dependencies from your package manager. Before running, you'll need to get your environment set up, by sourcing either setup.sh or setup.csh, depending on which shell you're using. The file will be in the top-level directory of LOOS if your working from a source tree, or in the top of the install directory (not the bin/ directory) if you're working from an installation.
- system file: This is the file that specifies the system's contents. This could be a PSF (CHARMM or NAMD), parmtop (Amber), gro (gromacs), xyz (Tinker), or a PDB file. LOOS is totally agnostic to which kind of file you use, except for the fact that the file formats have different information. So, if the tool you're using requires partial charges, you need to use a file format that contains that information (e.g. PSF). GRO is one of the less informative file formats, so we provide a tool (
gmxdump2pdb.pl) to generate a PSF for your gromacs system. Since PSFs contain connectivity information, this PSF is also useful for correctly rendering bonds of coarse-grained models in VMD. However, this PSF cannot be used for running a simulation, since it only contains the information LOOS needs.