Hicolm is an open source package focused in molecular modelling of condensed systems.
Below is a list of publications involving the HICOLM program:
F. W. Fernandes, HICOLM: High-Performance Platform of Physical Simulations by Using Low Computational Cost Methods. doi: 10.22456/2175-2745.92486.
To install just run "as a superuser" the script install.sh,
$ sudo ./install.sh
After that, HICOLM and auxiliary programs will be installed in the default PATH (/usr/local).
Notice: gfortran library is necessary to compile the Hicolm program and R packages to get the graphical support and the statistical analysis.
- Velocity Verlet integrator.
- Emulation of NVT, NPT and NVE ensemble by Berendsen or Nosรจ-Hoover barostat and thermostat.
- Implementation of Amber Protocol in Force Field. ๐
- Optimization method by steepest descent algorithm. ๐
After install the user must create in the working directory the following input files:
- Hicolm.in, with relevant informations about the structure, MD parameters and the force field:
# direct molecular dynamics
@MDRUNNING or @MDPREPARE
# System information
&STRUCT
...
&END
# MD parameters
&MD
...
&END
# Optimization parameters
&OPT
...
&END
# Force Field information
&FORCE
...
&END
The detailed description of each directive can be seen in doi: 10.22456/2175-2745.92486.
- Hicolm.sys, with coordinates and other information about each molecular type. Below is an example of H2O condensed system, the first line shows the quantity of molecular types, the second shows the molecular name, quantity of molecules and quantity of atoms of each molecule, respectively. Next shows types of each site followed by the partial charges. After that, the atomic number and the atomic coordinates of each atom are represented in next lines.
1
H2O 100 3
OW HW HW
-0.8340 0.4170 0.4170
8 5.29770100 12.22297800 19.92931800
1 4.72481900 13.03438700 19.81360300
1 5.30418400 11.42751000 20.53525100
...
After that, run the command hicolm
in your working directory. Four output files will be create:
- Hicolm.out: Contains relevant informations about the simulation;
- Hicolm.md: With values of energy, force, velocity and positions of each atom at each MD cycle;
- Hicolm.XSF: The latest force, velocity and positions of each atom in XSF format (see XCrysDen format);
- Hicolm.AXSF: Conjunction of frames containing force, velocity and positions in AXSF format.
For more information, you can run the examples in the examples directory, or send an issue in Issues page.