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Finding pathways from an Markov State Model.

This software package provides tools for finding pathways based on Markov statemodels. It is required to represent the matrix as an row-normalized matrix,where each row sums up to 1 and all entries are strictly greater 1.This package contains a proof-of-concept implementation of an suggestedalgorithm (see citations). If the matrix contains more than 100 highlyconnected states or a few hundred sparsly connected states the MCMC ispreferable.

The essential functions are:

• MSMPathfinder paths: see citation for further information
• MSMPathfinder mcmcsingle: Markov chain Monte Carlo propagation

For further information simply call both submodule with added-h flag.

All options are well documented and may be viewed byMSMPathfinder -h.

The underlying methods are based on the following article:

• D. Nagel, A. Weber and G. Stock,MSMPathfinder: Identification of pathways in Markov state models,J. Chem. Theory Comput., 16, 7874 (2020);DOI:10.1021/acs.jctc.0c00774

We kindly ask you to cite this article if you use this software package forpublished works.

This project was created bymoldyn-nagel.

Copyright (c) 2020-2021, Daniel NagelAll rights reserved.

Redistribution and use in source and binary forms, with or withoutmodification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice,this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,this list of conditions and the following disclaimer in the documentationand/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANYEXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIESOF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENTSHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENTOF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, ORTORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

required:

• BOOST >= 1.49
• cmake >= 2.8
• arecent C++ compiler (e.g. GNU g++ >= 4.9, mustsupport C++11 standard)

To quickly get a working binary

# clone the repogit clone https://github.com/moldyn/MSMPathfinder.git# create a build folder inside the code directorycd MSMPathfindermkdir build# change to the build directory and prepare make# if installition is not desired you can execute "cmake .." insteadcd buildcmake .. -DCMAKE_INSTALL_PREFIX=/my/installation/path# then compile and install the package to /my/installation/path# (or any other path you chose above) by invokingmakemake install