Deprecated: please see new documentation site.


About

"Amber" refers 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.

Amber is developed in an active collaboration of David Case at Rutgers University, Tom Cheatham at the University of Utah, Tom Darden at NIEHS, Ken Merz at Florida, Carlos Simmerling at SUNY-Stony Brook, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals. Amber was originally developed under the leadership of Peter Kollman, and Version 9 is dedicated to his memory.

On-line resources are available at the developer's site.

Version and Availability

Amber 10 is currently available on all LONI x86 clusters. Amber 11 is currently available on Queenbee and Eric.

Usage

You will need to add the following keys to your software environment:

> cat ~/.soft
+amber-10-intel-11.1-mvapich-1.1
+mvapich-1.1-intel-11.1
...

and execute the command resoft.

Note for TeraGrid users: the "+mvapich-1.1-intel-11.1" key must appear before any "@teragrid-xxx" macros.

An example job submission script is given here:

#!/bin/bash
#PBS -q checkpt
#PBS -A YOUR_ALLOCATION
#PBS -l nodes=X:ppn=8
#PBS -l walltime=HH:MM:SS
#PBS -j oe
#PBS -N NAME

cd $PBS_O_WORKDIR
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
mpirun -np $NPROCS /usr/local/packages/amber/10/intel-11.1-mvapich-1.1/bin/sander -O \
 -i my.in -o  my.out -c my.inpcrd -p my.prmtop -r my.rst

Users may direct questions to sys-help@loni.org.

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