This is a README pertaining the changes made to implement Random Acceleration Molecular Dynamics in Amber8. Changes in source code have only been made to sander. To test, if the code is working, a case was installed in the test directory (test/ramd). For an introduction to how to use RAMD in AMBER8, two examples can be found in the examples directory: ramd_expulsion and ramd_docking. Instructions on usage are included in the READMEs in the corresponding directories. You can find a README.ramd and a CHANGES.ramd file in the src/sander subdirectory, pointing out and explaining the changes to the source code. The code was written by Tim Johann, EML Research gGmbH, Heidelberg, Germany. It is based on a former implementation in AMBER7 by Dr. Ting Wang and Dr. Sudarko (both EML Research) as well as on ideas of Dr. Petr Kulhanek (Dept. of Chemistry, Masaryk University, Brno, Czech Republic). The method has been described in: - Luedemann,SK, Lounnas, V and Wade, RC: How do Substrates Enter and Products Exit the Buried Active Site of Cytochrome P450cam? 1. Random expulsion molecular dynamics to investigate ligand access channels and mechanisms. J. Mol. Biol. 303, pp. 797-811 (2000). - Johann, T: Perturbation Methods in Molecular Dynamics Simulations with Implicit Solvent Models. Diploma Thesis 2005, University of Heidelberg, Dept. of Physics and Astronomy. 2005/12/07 Tim Johann , EML Research gGmbH, Heidelberg, Germany.