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MOPAC

Introduction

MOPAC (Molecular Orbital PACkage) is a state-of-the-art, general-purpose NDO (Neglect of Differential Overlap) semi-empirical quantum chemistry program developed by James Stewart. Versions prior to and including MOPAC 7 are in the public domain. They include the classic NDO methods such as MNDO, AM1, PM3 and are mostly applicable to the study of the reactivity of molecular systems. More recent versions of MOPAC became closed-source, commercial products. The current version is MOPAC2016, which includes the newest semi-empirical methods such as RM1, PM6, dispersion and hydrogen bonds corrected variants PM3-DH+, and PM7.  It also offers the possibility for modeling of solvated molecular systems, periodic systems (slabs, solids, etc.) and very large molecules using the MOZYME method. MOPAC2016 code has an official website, http://openmopac.net.

Licensing and access

MOPAC 7 can be accessed freely, but, has not been installed on WestGrid. Later versions, such as MOPAC2012 and MOPAC2016 have been centrally installed for approved researchers who can agree to license conditions given below.  Alternatively, if you want to install your own licensed version of MOPAC, see the installation hints in the next section.

Versions of MOPAC installed on WestGrid are listed under the Software Versions tab.

Access to the centrally-installed code is controlled via membership in the wg-mopac UNIX group.  If you can agree to the license conditions and want to be added to that group, send an email to support@westgrid.ca confirming that you understand and agree to the following terms:

  • Your usage of MOPAC is bona fide academic.
  • You agree not to redistribute and give access to the MOPAC code to anyone else.
  • You agree to cite code and method references for your work done with MOPAC.
  • Should your usage change from academic to another type that does not confirm to "bona fide academic" you will inform us immediately, stop using this MOPAC installation and contact a MOPAC reseller as described on the MOPAC website.

Note that the closed-source binaries get updated every year by the MOPAC author, so, we can update them on user's request.

Individual installation of MOPAC on Westgrid

Individual researchers who have filled in the form at the MOPAC web site to obtain an academic license key, may download and install the software in their own directories. Due to the nature of the MOPAC distribution, each user has to accept the conditions and obtain his installation license key individually.

Here are some notes based on experience installing the software on the Grex cluster:

  • An appropriate Linux 64-bit version of MOPAC2016 should be selected; builds for CentOS-5 or 6 are a best bet. Builds for newer Linux distributions may not work on Grex because it requires GLIBC 2.14 or later, which is not currently available on Grex or other WestGrid systems.  (Many WestGrid systems have GLIBC 2.12).
  • After it has been confirmed that the requisite libraries are in place and a license key has been obtained, one can install the software, following the instructions from the MOPAC site. One minor change from the instructions given there is to replace references to the /opt directory with your home directory.  This is conveniently done by replacing /opt/mopac with $HOME/mopac in the instructions, and setting the MOPAC_LICENSE environment variable to $HOME/mopac.
  • MOPAC2016 uses a threaded version of the Intel Math Kernel Library (MKL). Therefore, the Intel OpenMP runtime library should be in LD_LIBRARY_PATH, and values for OMP_NUM_THREADS or MKL_NUM_THREADS environment variables have to be set to the value ${PBS_NUM_PPN} to match the ppn value given in the corresponding TORQUE job's CPU (nodes=1:ppn=N) request.
  • Although the installation instructions suggest creating mopac as an alias, it might be better to create it as a symbolic link instead, for aliases sometimes fail to propagate into the TORQUE batch jobs on compute nodes.

For More Information

2014-10-06 - First version of Grex's site wide installation/access.
2014-09-09 - Added note regarding installation of MOPAC2012 and the new license arrangement.
2017-04-10 - Updated documentation to include MOPAC2016.