3D-RISM Molecular Reconstruction
================================

This directory includes input files to produce water and thermodynamic
distributions around Factor Xa with 3D-RISM and the resulting output
files.  Both site and molecular distributions are produced.

Running the script
------------------

Output files may be reproduced using the `run.sh` script.  The script
requires AmberTool 19.4 or higher and for `$AMBERHOME` to be set.  By
default, the script will run on a single core.  To run in parallel,
ensure that AmberTools has been build with the `-mpi` and `-rism`
options and that the `$DO_PARALLEL` environment variable has been set.  E.g.,

export DO_PARALLEL='mpiexec -np 4'

Input files
-----------

The input files are

`fxa-strip.parm7` :
    The Amber parameter/topology file for factor Xa.
`fxa-strip.nc` :
    An Amber NetCDF trajectory file for factor Xa.  Contains only one
    frame.
`fxa-strip.pdb` :
    A PDB coordinate file for factor Xa.
`cTIP3P_pse3.xvv` :
    1D-RISM XVV file for cTIP3 water using the PSE-3 closure.

Output files
------------

The primary output file is

`rism.out` :
    Primary output file for `rism3d.snglpnt`.  It contains all of the
    settings, timings, memory use, and global solvation thermodynamic
    values.

The remaining outputfiles are volumetric distribution files, named
according to the following format:

    <type>.<structure>.<frame>.<format>

### `<type>`

One of 

`g` :
     Pair distribution function.

`g_dT` :
     Temperature derivative fo the pair distribution function.

`exchem` :
    The excess chemical potential.

`solvEne` :
    The total solvation energy.

`potUV` :
    The solute-solvent potential energy.

`entropy` :
    Solvation -T∆S.

### `<structure>`

Maybe the the solvent site name (e.g., `O` or `H1`), sum of all
solvent sites (omitted), or `mol` for the molecular reconstruction.

### `<frame>`

Always '1' in this examples.

### `<format>` 

The [DX
format](https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html)
is used in all cases and specified by 'dx'.