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manual.doc
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# Manual of Py_CpH-MD
Py_dCpH-MD: An open source python framework for discrete constant-pH molecular dynamics
========
Py_dCpH-MD realizes the discrete scheme of the constant pH MD methodology [1]. The code plugs into GROMACS [2] MD package.
The algorithm ensures that the charge of the simulation box is kept neutral during the simulation.
Unpack the compressed file with the following command:
tar -zxvf d_CpH-MD.tar
Requirements
------------
Please make sure that you have installed in your computing system the following libraries:
- Python 2.7,
- Numpy and Scipy
You can check where is python or which python, with the following command:
* python -c 'import numpy; numpy.test()'
* python -c 'import scipy; scipy.test()'
Also open the source code of d_CpH-MD.py using your favorite editor (vim, emacs, notepad)
and set up corretly the path to the directory where Gromacs is installed.
Installation
------------
Unpack the compressed file with the following command:
tar -zxvf d_CpH-MD.tar
Usage
-----
Look how easy it is to use:
./d_CpH-MD.py CpH_MD.inp >& CpH_MD.log &
Features
--------
- Be awesome
- Make things faster
* The code is implemented to work with GROMACS MD package, but it can easily be integrated to other MD engines.
Contribute
----------
- Issue Tracker: github.com/$project/$project/issues
- Source Code: github.com/$project/$project
Support
-------
If you are having issues, please let us know.
We have a mailing list located at: [email protected]
License
-------
The project is licensed under the ??? license.
References
----------
[1] \bibitem{1} R.~B{\"{u}}rgi, P.~A. Kollman, W.~F. Van~Gunsteren,
Simulating proteins at constant ph: An approach combining molecular dynamics and monte carlo simulation,
Proteins 47~(4) (2002) 469--480.
[2] \bibitem{2} B.~Hess, C.~Kutzner, D.~van~der Spoel, E.~Lindahl,
{GROMACS} 4: Algorithms for highly efficient, {Load-Balanced}, and scalable molecular simulation,
J. Chem. Theory Comput. 4~(3) (2008) 435--447.
=======
# Manual in simple ASCII format
>>>>>>> 16c45edd3bd03c0dea0592b8e6307d3e0066d7a3