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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.
- 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
- 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.
- Here <MDD File> is the input file (output from Step 5)
- <No of Components> is the maximum number of either
N or
C-HSQC
peaks in each region of the spectrum + 10-20% in most cases (such
as
N-NOESY-HSQC, CBCA(CO)NH or HCCH-TOCSY). It is a safe bet
to have more components than necessary.
- 0 - A zero (ask no questions!)
- <Max Iterations> is the number of iterations you wish to perform.
Somewhere between 250 and 500 is usually a good number. You can always
continue with more iterations if necessary
- <Eps> is a convergence criterion. Use 0 (or 1e-8)
- <Lambda> is the Tikhonov regularization parameter. Use 0.01
- <random seed or initial solution> is either a file containing initial
approximation (i.e. if you restart a calculation after a blackout
or just want to add more iterations) or a random positive integer
- <reserved memory> is given in Mb. Necessary to store both the data
and solution. Increase if your calculation crashes without starting
the iterations.
- 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>'
- <No of Components> is the total number of corresponding HSQC peaks
in the spectrum + 10-20%
- <No of Processors> - obvious, no? Anything above 1
- Note that there is no zero after the number of components and that
parameter <Eps> is also absent
- Other parameters are the same as for a single processor run
- 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: Converting back into NMRPipe
Up: README
Previous: Convert NMRPipe File into
Aleksandras Gutmanas
2009-01-26