Amber

Description
	Amber is the collective name for a suite of programmes that allow users to carry out molecular dynamic simulations.
Site	Version (Latest: v10.0)	Notes
ngs.rl.ac.uk	v10.0 (v9.0)	v9.0 includes bug fixes 1-35, v10.0 includes bug fixes 1-8
ngs.leeds.ac.uk	v10.0 (v9.0)
ngs.wmin.ac.uk	v10.0

On this page:

1. License
2. Running on the NGS (general)
   • Submission using the UI-WMS
   • Submission using the NGS portal
   • Submission using Globus
3. Compilation Information
4. Further Information

License

Amber is commercial software, paid for by the individual partner sites offering it. For example on ngs.rl.ac.uk this charge is paid for by STFC eScience Dept (SCT group) at R.A.L.. Binaries may not be copied from their installed location and the source code is not made available to NGS users.

Users of Amber on the NGS must credit the code authors where applicable, as well as crediting the NGS accordingly. We also ask that you credit the NGS site(s) where your Amber jobs are run - such as the STFC eScience Centre (RAL) - for providing access to the code.

In order to access Amber on the NGS, you should first contact the NGS helpdesk, agreeing to the above conditions, and wait for confirmation that privileges have been setup to run the code.

Running the Amber on the NGS (General)

There a multiple ways in which jobs can be launched on the NGS. In the examples below the input files described are available on the ngs.rl.ac.uk node. Copy all the input files, using globus-url-copy or similar, from:

gsiftp://ngs.rl.ac.uk:2811/apps/amber/examples/serial_example

or

gsiftp://ngs.rl.ac.uk:2811/apps/amber/examples/parallel_example

directories respectively for serial or parallel/mpi sander runs.

There is also a pmemd parallel example at:

gsiftp://ngs.rl.ac.uk:2811/apps/amber/examples/pmemd_example

• Submission Using the UI/WMS

  There is a UI-WMS Amber tutorial that covers the sander serial and pmemd MPI examples in more detail. The following outlines the general format of a JDL file for an MPI sander.LES.MPI run. The UI-WMS will choose the least loaded site which has Amber isntalled to run your job. It will automatically up and download your input and output files to the UI/login machine.

  To submit the sander.LES.MPI Amber example job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

  glite-wms-job-submit -o jobIDs -a amber.jdl

  Type = "Job";
  JobType = "mpich";
  Executable = "/usr/ngs/AMBER";
  Arguments = "sander.LES.MPI -O -i md.in -o md3.out -p les.top -c les.crd -x mcrd -inf mdinfo -r mdrestrt";
  CpuNumber = 4;
  StdOutput = "std.out";
  StdError = "std.err";
  Myproxyserver= "myproxy.ngs.ac.uk";
  InputSandbox = {"md.in","les.crd","les.top"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/amber";
  OutputSandbox = {"std.err","std.out","md3.out"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/amber";
  Requirements = (
       member("NGS-UEE-AMBER", other.GlueHostApplicationSoftwareRunTimeEnvironment)
  );
  Rank = other.GlueCEStateFreeCPUs;
  ShallowRetryCount = -1;

• NGS Web Portal Submission

After logging in to the NGS Portal, select the "Amber" template under the " Chemistry" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus

  To submit a serial Amber job use the following command (one line. You should not include the backslashes):

  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf '&(jobtype=single) \
  (executable=/usr/ngs/AMBER_10_0) \
  (arguments=sander -O -i in.md -c crd.md.23 -o cytosine.out)'

  • This runs amber v10.0. To run v9.0 use AMBER_9_0 instead of AMBER_10_0

  To submit a parallel Amber job use the following command (one line. You should not include the backslashes)

  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf '&(jobtype=mpi)(count=4)(executable=/usr/ngs/AMBER_10_0) \
  (arguments=sander.LES.MPI -O -i md.in -o md3.out -p les.top -c les.crd -x mcrd -inf mdinfo -r mdrestrt)'

This runs amber v10.0. To run v9.0 use AMBER_9_0 instead of AMBER_10_0

The default version of amber (using /usr/ngs/AMBER) is v10. To use version 9 use /usr/ngs/AMBER_9_0

Compilation Information for ngs.rl.ac.uk

Amber 9 uses AmberTools v1.0 and was compiled using

• PGI 6.2 Compilers.
• Scali MPI Libraries.Amber supplied lapack and blas Libraries.
• Bug fixes 1-35 are applied. 

Amber 10 uses AmberTools v1.2 and was compiled using

• PGI 7.2.3 Compilers.
• Scali MPI Libraries.
• Goto blas v1.09 Library.
• Bug fixes 1-8 are applied. 

Further Information

• Amber Home Page
• The Amber Mail Reflector 
• Amber 9 User Manual (pdf)
• Amber 10 User Manual. (pdf)