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                         README for SMOG2_tutorial


SMOG2_tutorial is a repository made to support everyone who wants to start 
working with Structure-Based Models generated with the SMOG 2 package.
More information about the SMOG 2 package, its manual, codes, and other 
examples can be found at smog-server.org.

SMOG2_tutorial is an AGPL-3.0 licensed repository. See LICENSE for more details.

This distribution contains the input and some output files obtained while 
simulating the Chymotrypsin inhibitor 2 (CI-2) dynamics over a range of 
temperatures to check some of its properties. Most results are due to an 
all-atom representation of CI-2, where all non-hydrogen atoms were depicted by 
spheres of unit radius. 

The file "roadmap.txt" contains the set of commands to reproduce all the 
results.
These commands were used in a Linux-based system, though small changes should 
be needed to use them in any Operational System. Each command (or set of 
commands) is preceded by comments on how they operate or what should be 
expected from it/them.

To evaluate the number of native contacts formed at each frame, it is used a 
python3 script called "contacts_chunk.py". The requirements to run it are 
described in the file "requirements.dat", which can be used alongside pip or 
conda/miniconda to install the libraries.

The file "2ci2.pdb" is the CI-2 structure downloaded from the PDB web server 
without any change. The other PDB files are modified versions, obtained 
following the steps presented in the "roadmap.txt"

The folder AA contains all the input files used in the simulations. The force 
field files are there, with some output files acquired using the roadmap given. 
Most heavy files were not kept to save the repository space (XTC, TRR, EDR, and 
LOG files). Others have to be divided to comply with GitHub's storage policy.

All comments, suggestions, questions, or feedback are welcomed. 
Please reach out through the repository channel or by e-mail.

IMPORTANT: type "git submodule update --init" to load all submodules needed.

Suggestion: the up-to-date "roadmap.txt" file should be used to generate the 
outputs, as it got some corrections along the path. The simulation results one 
may get after each iteration might be similar to the commits of this repository. 
As a random seed was chosen in GROMACS, one may get results that are not binary 
equal to the repository, though the analysis should give the same overall 
picture.

To pull a specific simulation iteration (commit), you may type:
"git checkout #commitnumber"
where #commitnumber must be, in this case:
cb44a85 -> for the first iteration
57e8b2f -> for the second iteration
1dee164 -> for the third iteration
dd6c59c -> for the fourth iteration
8fe9489 -> for the fifth iteration
8ae7b1f -> fot the sixth iteration
5ce27cb -> for the seventh iteration

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