PROFASI  Version 1.5
BasicMCRun program reference

The program BasicMCRun performs canonical Monte Carlo simulations on single or multiple chain systems at a constant temperature using the ProFASi libraries. It also forms the base for programs like simulated annealing, simulated tempering, parallel tempering.

Example use:

BasicMCRun --add_chain 1 "*GEWTY DDATKT FTVTE*" -ncyc 100000 -nrt 1000 -T "300 Kelvin"

In the above example, BasicMCRun was asked to perform a short simulation of 100000 MC sweeps for a 16 residue peptide (residues 41–56 of 1GB1.pdb), at 300 Kelvin. The program was asked to write to the run-time history file "rt" every 1000 sweeps.

The progam accepts a large number of options which can be given as command line arguments or in a settings file. This file is called "settings.cnf" by default, although this name can be changed using a command line option "–settings_file yourfilename". All command line options in their long form can be used as settings file instructions. For instance, the above run could have been done with the following settings.cnf file:

add_chain 1 * GEWTY DDATKT FTVTE *
num_cycles 100000
rt_write_freq 1000
temperature 300 Kelvin

With a file called "settings.cnf" with the above content, one can start BasicMCRun without any command line arguments with exactly the same effect as in the first example above. Notice that the quote marks in the command line example above have been dropped in the settings file. Also, those familiar with older versions of ProFASi will recognize that the sequence is no longer enclosed in angle brackets <>. It does not hurt to write the sequence in the old way, i.e., "add_chain 1 <* GEWTY DDATKT FTVTE *>", but it also does not do any good. In older versions of ProFASi, sequence input continued until the termination of the angle brackets, so that the sequence could be written in many lines. Now, sequence reading continues till the end of the line. If the sequence is long, and you want to write it in many line, you must use a continuation character "\", as shown below.

add_chain 1 * GEWTY \
              DDATKT \
              FTVTE *
num_cycles 100000
rt_write_freq 1000
temperature 300 Kelvin

Notice also that in the settings file, we use the long forms of the commands: "temperature" instead of "T". On the command line, the temperature can be specified using –temperature "300 Kelvin" or -T "300 Kelvin". But only the long form is recognized in the settings file.

The complete list of options accepted by the program is very long. But they can be grouped into a few categories. BasicMCRun accepts

In addition, the following miscellaneous instructions control various aspects of a run with BasicMCRun.

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2