Organize Files into MutInf’s official directory structure

You will give the program an option, “-x <base_directory>”, to tell MutInf which directory is your “base directory”: this directory will have subdirectories containing your files with dihedral angles for each residue.

This program uses an undersampling correction based on correlations between torsions in different simulations or different equal-sized blocks from one or more long simulations.

Ideally, six or more simulations or simulation blocks are ideal.

Place the dihedral angle .xvg or .xvg.gz files under directories named /dihedrals/g_chi/ under each run or “block”, unless the -d option is used to specify which subdirectory (if any) the torsion angle reside in beneath the base directory. The directories for each run or block are to be named “run1”, “run2”, “run3”, etc. in sequence.

For example, if "-d /" is used (I recommend this) then the torsion angle files would be in the run1 to run6 directories just beneath your base directory.

Example: If options “-x ~/md/wildtype/ -d /” are used, then your directory structure will look like this:

~/md/wildtype/

run1/

*.xvg.gz

run2/

*.xvg.gz

run3/

*.xvg.gz

…..

This program currently assumes that all simulations or blocks are of equal length. Any snapshots beyond the minimum block length are not analyzed (While in principle the code is general enough to handle differences in lengths of simulations/blocks, this feature is not currently enabled).

In the paper I used 50,000 snapshots at 0.1ps, over five simulations started from different random number seeds.
If you have one to a few long simulations, split them into six to ten"blocks" of 10-100ns each,
treating each as a separate simulation (the torsion angles should go in directories named run1, run2, run3, run4, run5, etc). This is so my correction for non-independence of the “blocks” can do its work.