molsim - Molecular dynamics with GNU Octave
molsim supports simulations of
- simple Lennard-Jones systems,
- molecular systems with bond, angle, and torsion potentials,
- confined flow systems, eg., Couette and Poiseuille flows,
- charged systems using shifted force and Wolf methods,
- dissipative particle dynamics systems,
- different ensembles,
- and more . .
Installation
At the Octave prompt simply use the command
>> pkg install "https://github.com/jesperschmidthansen/molsim/archive/refs/tags/v<version>.tar.gz"
where <version> is the version number. NOTE: Depdending on your system you may recieve warnings like
note: expected 'const mwSize *' {aka 'const long long int *'} but argument is of type 'const long int *'
These warnings are not always harmful and not a molsim issue. Proceed with care.
An example
An example of an NVE water simulation script ```octave nloops = 1000; temp0 = 298.15/78.2; cutoff= 2.5; sigma=1.0; epsilon=1.0; aw=1.0; cutoff_sf = 2.9; lbond = 0.316; kspring = 68421; angle = 1.97; kangle = 490; molsim('set', 'cutoff', cutoff_sf); molsim('set', 'timestep', 0.0005); molsim('set', 'exclusion', 'molecule'); molsim('set', 'omp', 4); molsim('load', 'xyz', 'sys_water.xyz'); molsim('load', 'top', 'sys_water.top'); for n=1:nloops molsim('reset') molsim('calcforce', 'lj', 'OO', cutoff, sigma, epsilon, aw); molsim('calcforce', 'coulomb', 'sf', cutoff_sf); molsim('calcforce', 'bond', 0, lbond, kspring); molsim('calcforce', 'angle', 0, angle, kangle); molsim('integrate', 'leapfrog'); end molsim('clear'); ```IMPORTANT NOTE: The 'sys_water.xyz' configuration file and 'sys_water.top' topology file must be in same directory from where you execute the script. They can be found under the project's resource/ folder
For further explanation check out the package tutorial under the project's doc/ folder
Contribution
I encourage anyone who uses or plans to use molsim to submit problematic issues - this includes issues regarding the documentation. I also welcome contributions to the code for the project, whether it is core features (seplib), post simulation data analysis programs, or extending the molsim wrapper.