Amber

Amber is a molecular dynamics software package. It was installed on Bellatrix in October 2013.

Versions
Amber 12 with AmberTools 13 has been compiled with Intel compilers and the Mvapich2 MPI.

Other versions can be installed if needed or available. Please contact Daniel Jana, the maintainer of Amber on Bellatrix, for that.

How to use it
First you have to load the module. You can do it with: $ module load amber/12-tools13-intel-mvapich2

This sets the right environment to use Amber, including the modules for the compiler and MPI.

To run Amber you will then proceed as you would usually do on your personal computer or cluster.

Since parallelization is quite efficient you'll probably want to use a line like:
 * 1) PBS -l select=2:ncpus=16:mpiprocs=16:mem=10000mb

on the top of your script. This specific case asks for two sets of 16 CPU and 16 MPI processes with 10000 MB of RAM. The job, thus, asks for a total of 32 cores and ~20 GB of RAM. Any of these numbers can be changed, depending on your needs.

Do I have access to it?
It is available to all members of the amber-soft group. You can check if you are a member of the group by using the command "id". You will see something like: $ id uid=33333(myusername) gid=10111(myunit) groups=65115(dit-clusters-users),65359(bellatrix-users),64644(amber-soft)

You may have a different set of groups but you need amber-soft to be there. Trying to load the module without belonging to the group will result in a warning message.

How to get the right to use it?
If you are not part of the amber-soft group contact Daniel Jana. He'll inform you on how to be a member of the group.