Users.Main

MolDynSim Users' guide

The MolDynSim software (which is a part of the TrajLab project) can be used for molecular simulations involving an arbitrary number of molecular species, number of molecules per species, number of atoms per molecule and number of spatial degrees of freedom. It is based on the notion of intra- and/or intermolecular force fields (alias potential energy functions) which can be freely defined by the user. For technical details see the respective chapter of the developers' guide. Along with the gradient (vector) as well as the Hessian (matrix), the implementation and characterization of an appropriate force field is the central task in every MolDynSim simulation.

Programs

The MATLAB functions comprising the MolDynSim package are listed in the following:

• mol_Initialize: Set force field parameters and initial values for all MolSim programs

• mol_ScanPot_1D: Scan force field along specified direction

• mol_Optimize: Find minimum energy conformations of a molecular system

• mol_SortMinima: Sort minima stored in XYZ-files according to increasing energy

• mol_Vibrations: Find frequencies and spatial patterns of molecular vibrations

• mol_Dynamics: Numerical solution of equations of motion

• mol_MonteCarlo: Sampling a canonical distribution by random walking

Advanced techniques for analysis of molecular trajectory data, e.g. geometric and spectral clustering to detect and characterize metastable molecular conformations, can be found in the MetaStable subproject

General remarks

• Note that all MolDynSim functions use molecular units throughout.

• For a quick start of your projects using MolDynSim, see our demo examples.

• For more detailed information on MolDynSim force fields, data structures, algorithms, etc, see also our Developers' guide.

Visualization

Although there are some rudimentary fragments of MATLAB-based molecular visualization codes in the repository at SourceForge ('OldStuff'), it is recommended to use external codes for molecular visualization which should be interfaced through the XYZ files produced by our MolDynSim codes. Our recommendation is to use the VMD program which is highly flexible and available (free of charge!) for all major computing platforms (Windows, Linux, MacOS). VMD is being developed by Prof. Klaus Schulten's group at University of Illinois, Urbana, Champaign. Alternatively, you can use JMOL which is an open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.