KEYWORDS: CORE_CONCEPTS GENERAL
This size of a macromolecule constitutes a major restriction on what you can and can not do with Rosetta (or any other simulation software). There are two aspects where the number of residues in a structure matter:
The exact size limit depends on several factors:
Sampling means changing DOFs. The more DOFs need to be sampled, the more runs you will have to perform to get a reliable answer. There are two basic ways to increase sampling:
Note: You need to provide -out:prefix or -out:suffix options. Otherwise Rosetta would try to overwrite files produced by a parallel job -- in which case it will not do anything!
To avoid the problem of file naming and for not having to start multiple jobs with different output file names, you can also compile Rosetta for usage with MPI (see "Compiling Rosetta"). MPI (short for Message Passing Interface) executables can launch many parallel jobs and handle file naming for you.
However, the MPI version is intended for use on supercomputer clusters. There you can specify the number of processors for a job. Rosetta will then divide your -nstruct value by the number of CPUs.
Example: A snipped from a cluster submit file:
#SBATCH --ntasks=4 srun relax.mpi.linuxgccrelease -s input.pdb -nstruct 100
This will perform 25 relax runs on each of 4 CPUs. This is 4 x faster then -nstruct 100 on a single CPU.
Instead of producing a large number of pdb files, Rosetta can provide the strctural and energetic information for any number of structures into a so-called silent file. Additionally, these silent files can be in binary format, which reduces the required disc space. Rosetta provides tools for working with these files. Look at the "Analysis" section for information of how to work with silent files. A couple of applications, e.g. scoring, are able to handle silent files directly as input.
Rosetta produces a lot of output. For production runs it is recommended to swith that of for saving disc space. For finding out why on Earth your protocol continues to crash, however, you can also increase the level of detail that is shown.
Switch off all logging info:
The following options provide increasing amount of information output
-out:levels all:critical -out:levels all:error -out:levels all:warning -out:levels all:info -out:levels all:debug -out:levels all:trace
Note: The output can be written into a log file like this:
score.linuxgccrelease -s input.pdb > log.txt
Output for a wrong input file name
core.import_pose.import_pose: File: foo.pdb not found! ERROR: Cannot open file "foo.pdb" ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 268 [...] [ERROR] EXCN_utility_exit has been thrown from: src/core/import_pose/import_pose.cc line: 268 ERROR: Cannot open file "foo.pdb"