amber

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.

Amber 11 is compiled with AmberTools 1.4 and 1.5 (at1.5 in soft key)

Versions and Availability

Module Names for amber on smic
Machine Version Module Name
smic 14 amber/14/INTEL-140-MVAPICH2-2.0
▶ **FIX-ME** FAQ?

Usage

Make sure softenv keys are matched up with corresponding versions of the compiler and MPI library. For instance:

+amber-11-intel-11.1-mvapich-1.1
+mvapich-1.1-intel-11.1

Amber is normally run via a PBS job script.

▶ Open Example?

Note: the usual executable name used is sander (serial) or sander.MPI (parallel).

#!/bin/bash
#PBS -A my_allocation_code
#PBS -q checkpt
#PBS -l nodes=X:ppn=4
#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 -machinefile $PBS_NODEFILE sander.MPI -O \
   -i my.in -o  my.out -c my.inpcrd -p my.prmtop -r my.rst

Resources

  • The Amber Home Page has a variety of on-line resources available, including manuals and tutorials.

Last modified: November 11 2014 16:26:11.