Deprecated: please see new documentation site.


"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.

Version and availability

The parallel version of Amber 8.0 is currently available on Ducky. We are working to purchase a license of Amber 9.0, which is the latest version, for all LONI clusters.

Usage

Add the line below to your .soft file and resoft:

 +amber-8

Submit Amber jobs through Loadleveler. A sample script looks like:

#!/bin/bash
#@job_name=amber_min
#@job_type=parallel
#@account_no=loni_hybrid01
#@output=/work/default/lyan1/amber/amber.std
#@error=/work/default/lyan1/amber/amber.err
#@initialdir=/work/default/lyan1/amber
#@notify_user=lyan1@cct.lsu.edu
#@class=SP5L
#@notification=error
#@checkpoint=no
#@restart=no
#@wall_clock_limit=1:00:00
#@node_usage=shared
#@blocking=unlimited
#@total_tasks=8
#@requirements=(Arch=="Power5")
#@network.MPI=sn_single,not_shared,US,HIGH
#@queue
sander -O -i  my.in -o  my.out -c my.inpcrd -p my.prmtop -r my.rst


References

Amber website: http://amber.scripps.edu

User's manual (v8.0) : http://amber.scripps.edu/doc8/index.html

A good tutorial: http://amber.scripps.edu/tutorials


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

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