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A python interface for the GROMACS molecular simulation package.
Assembly C Shell Python
branch: master

README

*****************************************************************************************
* Welcome to GromPy, the python interface for the GROMACS molecular simulation package. *
*****************************************************************************************

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NOTES:
* GromPy is compatible to the modified source of GROMACS 4.0.5 (gromacs-4.0.5_HYBRID). 
  Alternatively, a patch for 4.0.7 is available, too.
* The current version of GromPy is tested on 32-bit (i386,ia32) Ubuntu Linux versions
  9.10 (Karmic Koala) and 11.04 (Natty Narwhal), and on 64-bit (x86_64,amd64) Debian
  Linux version 6.0.2 (Squeeze).
* Please let us know if GromPy is working on other distro's as well!

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In order to get GromPy to work, please proceed through the following steps.

* Compilation of the modified GROMACS source:
  - Unpack gromacs-4.0.5_HYBRID.tar.bz2 in a working directory;
  - cd gromacs-4.0.5_HYBRID;
  - ./configure --prefix=$PWD --enable-shared --with-gsl CFLAGS="-O2"
    (Note that the install directory of the necessary .so libraries will 
    become $PWD/src/kernel/libmdrun0 or $PWD/src/kernel/libmdrun1, c.f. 
    below);
  - make;
  - make install;
  - ./gen_libmdrun0.sh (to generate a statically linked library);
  - ./gen_libmdrun1.sh (to generate a dynamically linked library).
  - for a parallel install with other gromacs versions you can define e.g.

* Specify via environment variables which shared libraries to load:
  - By default, Grompy will load libmd.so libgmx.so and libmdrun.so for single precision
    and libmd_d.so libgmx_d.so and libmdrun_d.so for double precision from the linker search path.
  - Double precicion is turned on by setting the GROMPY_DOUBLE environment variable.
  - Specifying GROMPY_LIBEXT allows a parallel install of the libraries e.g. libgmx_grompy.so from 
    the modified source and from libgmx.so used for the simulations.
  - Loading of each individual library can also set by GROMPY_LIBGMX, GROMPY_LIBMD and 
    GROMPY_LIBMDRUN. E.g. GROMPY_LIBMDRUN="~/src/gromacs-4.0.5_TEST/src/kernel/libmdrun0/mdrun.so"

The GromPy directory contains the python module that enables GCMC.
It is important to correctly set the path to the gromacs dll in
__init__.py, lines 26/27. The python code is a bit messy but should be
readable enough. We hope improving this as soon as possible.

The TestMuVT directory containis a shell script as an example of
how to run the python module. The testsystem is a LJ fluid @ T=900K
(MARTINI FORCEFIELD).

In general, before running there is an important preprocessing step: You
should have a tpr file for eacht configuration you would like to sample,
c.f. directory "tpr"). The function mdrunner() is split up into three
parts: init, integrate en finalize. The communication between these
parts proceeds through a communication data structure that contains all
necessary member data structures. For GCMC the most important ones are
the velocity and coordinate arrays.

The starting configuration (tpr) should contain no particle overlaps. For
the TestMuVT directory this means that one should choose a GROMACS start
configuration WXXX.tpr with XXX<400. Tpr files with a higher number of 
molecules contain atomic overlaps and can therefore not be used as 
starting configuration. At run time the content of the tpr file is allowed
to have overlaps, since the coordinate and velocity arrays are copied from 
a previous one, after which a trial particle insertion or removal is
applied.

Good luck!

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DISCLAIMER:
This code is NOT error-proof. Please notify us if you run into any problems.

------

=====================================================
René Pool

Division of Molecular and Computational Toxicology
Department of Chemistry and Pharmaceutical Sciences
Vrije Universiteit Amsterdam
De Boelelaan 1083
1081HV AMSTERDAM, the Netherlands
-----
IBIVU/Bioinformatics
Department of Computer Science
Vrije Universiteit Amsterdam
De Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands

E: r.pool_AT_vu.nl
=====================================================

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