Accelrys Materials Studio on MCSR Systems

MCSR is pleased to announce the addition of Accelrys Materials Studio to its current list of software available to MCSR researchers. Materials Studio consists of several modules of simulation, cheminformatics, and bioinformatics products that span drug discovery from target identification and candidate evaluation to compound management and development engineering, all of which could be purchased separately per module. Materials simulation and informatics products that support product and process development in the chemicals and materials-based industries are also available.

Materials Studio ver. 3.2 was first installed on sweetgum 18 months ago with temporary license to be tested by the chemistry/biochemistry researchers from Jackson State University and The University of Southern Mississippi as well as Civil Engineering Department of University of Mississippi. After the purchase of several modules by the Civil Engineering Department at the University of Mississippi and two modules by the Chemistry and Biochemistry Department at The University of Southern Mississippi, we have upgraded to Materials Studio 4.0 with a permanent license for the modules purchased. Thus, currently, MCSR maintains floating licenses for these six Materials Studio modules: VAMP, DMol3, Discover, Compass, DPD and Amorphous Cell, some of which are available for use on up to 127 CPUs at a time (across all MCSR systems and users.) The list of the modules as well as the cpu licenses for each module are shown below:

As shown above, the licenses for modules Discover, Compass, DPD, and Amorphous Cell have been purchased by the proposal grant of Prof. Ahmed Al-Ostaz whereas the licenses for modules Dmol3 and Vamp have been purchased by the proposal grant of Prof. Paige Phillips; hence any researcher affiliated with these researchers has the priority of usage of Materials Studio in our systems. For more information on Accelrys and white papers on research, please visit Materials Studio of Accelrys.

Using Materials Studio with PBS on MCSR Systems

Currently, Materials Studio, MSI, version 4.0 is installed sweetgum and mimosa. Within the next month, the installation of MSI on redwood will be completed, and a script will be written by MCSR consultants for the submission of Materials Studio calculations. This script, similar to the g03sub script for submitting Gaussian 03 calculations, will do some error checking and then create and submit a PBS job to run your calculation, injecting a two-digit code into the PBS job name, so that our PBS jobs datawarehouse will recognize your job as a Materials Studio calculation of a given module, and allow this job to distinguishable from others in the My MCSR Jobs portal. In the meantime, you will need to write your own PBS scripts to run the calculations, and encode your PBS jobname as described further below. MSI has been installed under the directories /usr/local/apps/MSI and /usr/local/appl/MSI in mimosa and sweetgum, respectively. There are two test folders, one each for "Discover" and "Dmol3" modules, located under the MSI directory under the MSI_testjobs folder. Each folder contains essential input files for each module and a pbs script to run the jobs. You can simply submit these jobs via qsub command of PBS after copying the folders and files to your account directory and modifying "cd " lines of pbs files by changing the directory paths to your account path. You may follow the steps below to run Discover test on sweetgum:

Once you login to the system, you will receive a command prompt as sweetgum % , then please follow the steps below;

• Change directory to your /ptmp directory: cd /ptmp/(your_login_name)
  (In this example, we did the steps for user: tpirim)
  cd /ptmp/tpirim
• Copy the test folders to your ptmp directory:
  cp -Rf /usr/local/appl/MSI/MSI_testjobs .
• Change directory:
  cd MSI_testjobs/Discover
• Edit discover.pbs via the pico text editor:
  pico discover.pbs
  
• Change the line "cd /usr/local/appl/MSI/MSI_testjobs/Discover" to "cd /ptmp/(user login name)/MSI_testjobs/Discover":
  cd /ptmp/tpirim/MSI_testjobs/Discover
• Press Ctrl-X to save the discover.pbs file and exit the pico text editor.
• Submit the job via qsub command of PBS:
  qsub discover.pbs
• Follow your job using qstat command:
  qstat -a
  For more information on PBS command, please visit our PBS Tutorial Web Site.

Each Materials Studio job needs to have a specific name code assigned depending on the the module being used by adding the PBS command, "#PBS -N" in your script, i.e. For Discover test job above, #PBS -N Zstest command line has been added to the discover.pbs script. Hence, here are the PBS name codes need to be given according to modules:
Discover: ZSname_of_input_file
DMol3: Z3name_of_input_file
Amorphous Cell: ZAname_of_input_file
Compass: ZCname_of_input_file
DPD: ZDname_of_input_file
Vamp: ZVname_of_input_file

For more information on PBS commands, you may visit PBS Batch Script Web Site. For further information on Accelrys, please contact MCSR Consultancy Group via emailing assist at mcsr.olemiss.edu.