Supercomputer documentation is always a work in progress! Please email questions, corrections, or suggestions to the HPC support team at help-hpc@uky.edu as usual. Thanks!

For information on current problems and outages, see the News page.

See also the Amber Frequently Asked Question list.

Getting Started with Amber

Amber can refer to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

See the Amber Molecular Dynamics Package home page.

[Coming Soon]

For more information about Amber 12, see the Amber 12 New Features page.

The Amber 12 module name is "amber/openmpi/12p5".
"module avail" will show this.
After you load the module, you don't have to specify the full path any more.

If you want to do an MPI run, you need to use sander.MPI (sander is for serial run).

in .bashrc file: module load amber/openmpi/12p5

in submit script

# prog name
PROG=sander

# run programme
mpiexec $PROG -O -O -i MD100ps_bel.in -c ponVRtrpwt2ns.rst