ILRI Research Computing

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====== Amber Software Suite ======
Amber Software suite consists of Amber & Amber Tools. AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

===== Information =====

  * Versions: Amber 12 & AmberTools 13
  * Added: November, 2015
  * Link: http://ambermd.org/

===== Usage =====

See which versions of amber & ambertools are available:
<code>$ module avail amber
</code>

Load amber suite—includes both Amber 12 and Amber Tools 13:
<code>$ module load amber/12</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ tar -xvf AmberTools13.tar.bz2
$ tar -xvf Amber12.tar.bz2
$ cd amber12/
$ scl enable devtoolset-2 bash
$ sudo mkdir  -p /export/apps/amber/12
$ sudo chown joguya:joguya /export/apps/amber/12
$ module load python/2.7.8 openmpi/1.8.2
$ export AMBERHOME=`pwd`
$ ./configure gnu
$ DO_PARALLEL='mpirun -np 3' make test
$ make -j 4 install
$ cp -r . /export/apps/amber/12/
$ sudo chown -R root:root /export/apps/amber/12
</code>