CosSq

This is a C++ program to analyze orientations of water molecules from multiple-frame GROMACS structure files (*.gro). Fined-grained OpenMp is implented to fulfill parallel computing in multiple-processors computers.

Requirements

GROMACS

Preparing multi-frame .gro file

Use the trjconv tool installed with GROMACS to convert a trajectory file (.trr) into a multi-frame .gro file. Type

gmx trjconv -f *.trr -s *.tpr -n *.ndx -pbc whole -o sample.gro

A sample output "sample.gro" is provided for testing CosSq.

Running CosSq

We use make to compile and execuate CosSq in once.

make Makefile_CosSq_OpenMP

After the job finish, three output files will be generated:

sample.cos
sample.dip
sample.log

The sample.cos file prints out distant-dependent <cosθⁿ> of water (n=1,2,3,4). The sample.dip file gives the z-component of polarization density of water in along z-direction.

License

Copyright (C) 2017 Si-Han Chen chen.3262@osu.edu