Please note: The FAQ pages at the HPCVL website are continuously being revised. Some pages might pertain to an older configuration of the system. Please let us know if you encounter problems or inaccuracies, and we will correct the entries.
Amber is a suite of programs that allows the user to carry out molecular dynamics simulations. It is particularly well-suited for calculations on biomolecules. The suite consists of the following parts:
a. LEaP is a program to set up a new system or modify an existing one.
b. Antechamber is used to include standard nucleic acids or proteins.
c. Sander is the basic molecular dynamics / energy optimization program.
d. Gibbs is a free-energy perturbation program.
e. Nmode is used for vibrational analysis.
f. Anal is used for the structural analysis of a specific configuration of the system.
g. Ptraj analyses trajectories from a molecular dynamics run.
h. Carnal is an alternative molecular-dynamics analysis program (somewhat complementary to Ptraj).
i. Nmanal and Lmanal compute atomic fluctuations and correlation functions.
j. MM-Pbsa is a script file that performs an automatic analysis of molecular-dynamics "snapshots"
This list also gives a simple overview of the capabilities of Amber. The current version of Amber running on HPCVL machines is Amber 9. The most current version is version 11.