MSanalysis 1.0 release

Update 2017: Please contact the author to get the source codes, email: [email protected]

The most recent release can be download here:

The C++ source code of backend processing engine can be download here:

Quick and dirty install guide

MSanalysis has two way to get the input data: 1. Read from Gromacs output trajectory files, 2. Read from Gromacs output data directly. It's recommend to install MSanalysis in the same machine as Gromacs.

1. Get the latest version of your C and C++ compilers.
2. Check that you have CMake version 2.8.8 or later.
3. Install Gromacs. You can follow this guide to install Gromacs.
4. Install Django. You can use pip to install Django.

    pip install django

    You can see this guide for a detail information.

5. Install Apache2 and mod_wsgi.

    sudo apt-get install apache2
    sudo apt-get install libapache2-mod-wsgi

6. Install sqlite3.

    sudo apt-get install sqlite3

7. Download the source code of MSanalysis and extract it to a directory.
8. Add a new configure file for MSanalysis.

    sudo vi /etc/apache2/sites-available/msanalysis.conf

    Copy the following content to this file.

<VirtualHost *:80>
    ServerAdmin [email protected]
    Alias /static/ /path/to/msanalysis/static/
    <Directory /path/to/msanalysis/static>
        Require all granted
    WSGIScriptAlias / /path/to/msanalysis/msanalysis/
    <Directory /path/to/msanalysis/msanalysis/>
        Require all granted

    Active it.

    sudo a2ensite msanalysis

9. Restart Apache.

    sudo service apache2 restart

Modify Gromacs

You need to modify the souce code and rebuild Gromacs, so that Gromacs can write the output data to shared memory where MSanalysis can read from.

1. Replace /path/to/gromacs/src/gromacs/mdlib/mdoutf.cpp by this file: mdoutf.cpp
2. Rebuild Gromacs.

    cd /path/to/gromacs/build/
    make install
    source /usr/local/gromacs/bin/GMXRC

This project is supported by a NIH R01 grant (R01-GM086707) & a NSF grant (CAREER, IIS-1253980)

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