icemas

Icemas (Integration of the Classical Equations of motion of Molecules of Arbitrary Shape) is a C++ code to perform molecular dynamics (MD) simulations. The program has most of the basic features to be found in any MD package. If you look for high performance and/or a number of special features icemas is not your choice. Quite a few free software packages are available nowadays (e.g. NAMD, Gromacs, OpenMM, etc) most of which include functionalities and features that Icemas does not have. Icemas does, however, have the advantage of a very tidy and clearly structured source code (achieved by extensive usage of the C++ concept of operator overloading). It therefore might be useful for pedagogical purposes, i.e., for people that are new to the field and want to have a look at a readable source code. It could also be helpful as a basis for testing new algorithms, as the structure of the code is transparent, so that it is easy to make modifications, without causing undesired effects.

Features

• energy expression including Lennard-Jones, Coulomb, bond, angle, and dihedral angle terms
• Electrostatic long range interactions via Ewald summation
• NVE and NVT (Nose Hoover) ensembles
• SHAKE
• neighbour-list

Prerequisites

• A C++ compiler (recent versions of gcc on most Linux distros should work)

Installation

On Linux (tested on Debian and Ubuntu, but should work on most distros)

git clone https://github.com/mbatgh/icemas.git
cd icemas/src
make
sudo make install

The binary icemas should now be in /usr/local/bin

Usage

Have a look at the content of the examples folder for a quick start.

Generally three input-files are required:

1. A parameter-file called pars.name, where name is an arbitrary ID chosen by the user. A default-parameter-file with short explanations of all possible entries are explained can be found in the examples folder.
2. A system-file (name of which must be given in the parameter-file). It contains information such as number and type of molecules and force-field-parameters. Examples can be found in the system folder.
3. a file (name provided in the parameter-file) containing the initial-coordinates. Examples, and a tool to generate such files are provided in the coords folder.

Given these files the simulation is started on the command-line, by typing

icemas name [name] ...

If more than one names are provided as arguments icemas will do each of the named runs in succession.

Depending on the data in the parameter-file, Icemas will write several output-files in the diectory, it was started in.

data.name

this file contains the thermodynamic data. In order of columns:
  - simulation-time [ps]
  - temperature [K]
  - Pressure [MPa]
  - Virial [kJ/mol]
  - kinetic Energy [kJ/mol]
  - pot. Energy (VdW-interactions) [kJ/mol]
  - pot. Energy (real part of Ewald-sum) [kJ/mol]
  - pot. Energy (imag. part of Ewald-sum) [kJ/mol]
  - pot. Energy (due to bond-angles) [kJ/mol]
  - pot. Energy (due to dihedral-angles) [kJ/mol]
  - pot. Energy (due to improper-dihedral-angles) [kJ/mol]    
  - total Energy [kJ/mol]

r_out.name

The final coordinates

angdis.name, dhangdis.name, idhangdis.name

Files, containig distribution-functions for the (proper dihedral, improper dihedral) angles.

phsp.name

this file contains data quantifying the extent of a possible phase-separation. 

pcf.N.name

Pair-correlation-functions, where N is a number (1 up to the total number of pairs specified in 'pars.name')

Limitations

• Runs on CPU only (no GPU support)
• No automated generation of force field parameters (writing a simple script to transform topology files from other packages, such as Gromacs, Charmm, or Amber should be straight forward, though)

Contact

Please send any questions/bug-reports/suggestions to me. My full name is rare enough, so that, together with the place where I live (Graz), google will promptly provide you with my email address.