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[edit] HARLEM - Molecular Modeling Package
HARLEM ( abbreviation stands for HAmiltonians to Research LargE Molecules) was initially developed by Igor Kurnikov in 1999 while he was a graduate student and a postdoc in research groups of D. Beratan at the University of Pittsburgh and M. Ratner at Northwestern University. The first version of HARLEM was developed to study long range electron transfer reactions in biological systems and nanodevices. Eventually the scope of the program was extended to incorporate a variety of molecular modeling techniques and approaches. It has been used to study such diverse biological problems as oxidative stress in biology and ionic currents through membrane protein channels.
Currently, HARLEM is a multipurpose multi-scale molecular simulation package with unique capabilities not found in other programs. It also provides convenient graphical interface to a few popular molecular modeling packages such as AMBER and GAUSSIAN.
HARLEM is being actively developed and maintained by Igor Kurnikov and Nikolay Simakov in Maria Kurnikova research group at Carnegie Mellon University in Pittsburgh, PA (USA).
Please feel free to visit our web pages [1] for more information on research and how HARLEM has been used as part of the research.
The HARLEM Developer's guide provides a list of program capabilities, guidelines on developing computational modules within HARLEM, and also a reference to HARLEM's C++ classes structure and Python scripting interface.
You can browse System Requirements for HARLEM compilation. WINDOWS and Linux versions of the program are curently available. Image:Example.jpg
[edit] Getting started
[edit] Download and Install HARLEM on Windows
On windows:
0. If you are planning to use python scripting capability of HARLEM download and install python 2.5
1. Download harlem.zip
2. Unpack content of harlem.zip file into c: directory, this should create
- directory c://HARLEM with an executable harlem.exe and several dll files
- Subdirectory c://HARLEM/residues_db with residues and force-field databases (currently files amber_94_ff.dat, res_XXX.hlm files)
- Subdirectory c://HARLEM/scripts: with Python scripts providing access to HARLEM classes
- Subdirectory c://HARLEM/basis: with Gaussian Quantum Chemical basis sets in DALTON format
- Subdirectory c://HARLEM/doc: containing HARLEM documentation.
- Subdirectory c://HARLEM/examples with a few input files and scripts to run HARLEM jobs
3. If installation has been performed into the directory other than c: (for example d:\) please set environment variable HARLEM_HOME to this directory (SET HARLEM_HOME=d:\)
4. Include the directory c://HARLEM into your PATH enivronment variable, also add to path the directory containing Internet Explorer binary iexpore.exe, to be able to invoke manual from inside the program
Members of Kurnikova's group may download HARLEM with AMBER binaries from the Group Intranet (DOCman/Software)
[edit] HARLEM Documentation
[edit] HARLEM Tutorials
- Molecular Visualization
- Molecular Dynamics
- Monte Carlo method
[edit] Useful Python Scripts for HARLEM
- Overlap Script
- Calculation of pKa values
[edit] For Developers
- HARLEM Development and compilation on UNIX
- HARLEM on Linux and Windows, electrostatics via PNPS: PNPS instead of ElectrostMod
Application Programming Interface
This should contain the link to doxygen documentation
