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MDD Calculation

The actual MDD calculation is taken out of the GUI wizard because it can take a long time to perform and it may be annoying to keep the graphical program idling. In addition, you may wish to perform the calculation on a more powerful machine or a cluster. You should thus transfer the output file from Step 5 to the desired location and start the calculation. The detailed instructions are repeated in the information window of the user interface and are given here for reference. You can fill out the relevant fields below the information window, and press the CREATE COMMAND FOR CALCULATION button. This will create a file with the correct command, which you can run or copy into command line.

  1. If your dataset is large you may wish to login to the cluster. Please, check with your system administrators about the details of initiating a calculation on multiple processors
  2. For single processor, the command is 'MDDNMR1.2C <MDD FILE> <NO. OF COMPONENTS> 0 <MAX ITERATIONS> <EPS> <LAMBDA> <RANDOM SEED OR INITIAL SOLUTION> <RESERVED MEMORY>'. Parameters are explained below. The created script takes a file with the list of regions as an argument and automatically starts a calculation process for each region. Unless you know what you are doing, do not modify the file containing the list of regions as it is required for Step 7. If any process needs to be restarted, copy the list into another file and modify accordingly. You can, of course, use the general command and start each calculation in each subfolder.

  3. For multiple processors, the command is 'MPIRUN -NP <NO OF PROCESORS> MDDNMRP_UHN <MDD FILE> <NO. OF COMPONENTS> <MAX ITERATIONS> <LAMBDA> <RANDOM SEED OR INITIAL SOLUTION> <RESERVED MEMORY>'

  4. The result of the calculation is by default stored in file RES.DAT. Copy it to a file of your liking. This unfortunately puts a limitation - you may start only one calculation from each directory, as otherwise RES.DAT would get overwritten by multiple runs. RES.DAT may be used to restart the calculation as <random seed or initial solution> parameter above. Note that somewhat newer MDDNMR1.2C program (for single processor) produces a slightly different file format, which includes some comments and size information in the beginning. You do not need to be concerned with that unless you want to restart your calculation from a previous solution and switch from sinlge to multiple processors or vice versa.


next up previous
Next: Converting back into NMRPipe Up: README Previous: Convert NMRPipe File into
Aleksandras Gutmanas 2009-01-26