Difference between revisions of "GROMACS Plugin"

Type	PyMOL Plugin
Download	https://github.com/makson96/Dynamics/releases
Author(s)	Laboratory of Biomolecular Systems Simulations
License	GPLv3

Revision as of 06:43, 25 October 2017

Dynamics PyMOL Plugin is plugin for PyMOL, which add molecular dynamics simulation feature. It is meant to be easy to use. The plugin uses GROMACS tools as a back-end. Project is developed as an open source and as such create full open source stack together with PyMOL and GROMACS. Software works on Linux, MacOS X and Windows/Cygwin.

Website

https://github.com/makson96/Dynamics

Features

Easy to use GUI, to take advantage of complex software GROMACS.
Work directly on molecules loaded to PyMOL.
Display results of calculations directly in PyMOL.
Set restraints, choose water models, force fields and many more.
Save your work and finish calculations later or on the other machine.
Do your work free of charge and without any restrictions. Feel free to modify any component of the stack.
Minimum dependencies. Plugin use the same graphic libraries as PyMOL, so working PyMOL and GROMACS installations are enough to make plugin work.

Note that exact instruction of how to use program is in the software manual, which is available together with the plugin.

Installation

There are at least few ways to install the plugin. In this section we will describe the most common.

Ubuntu

The easiest way to install the plugin is to use PPA repositories:

sudo add-apt-repository ppa:makson96/dynamics
sudo apt-get update
sudo apt-get install pymol-plugin-dynamics

All required libraries will be downloaded as dependencies. Supported versions of Ubuntu are latest stable and latest LTS.

Gentoo

The plugin is also present in Gentoo ebuild system. To make the installation use (as root):

emerge --ask sci-chemistry/pymol-plugins-dynamics

Other Linux distributions and macOS

The second way for all other platforms, is to download latest release of the plugin directly from its GitHub webpage:
https://github.com/makson96/Dynamics/releases
Then run PyMOL as a root. On the top Menu choose Plugin->Manage Plugins->Install... Then choose pymol_plugin_dynamics.py file. After installation restart PyMOL with normal user privilege. On macOS you will need to use X11 Hybrid version of the PyMOL.

Required dependencies:

PyMOL
GROMACS
ProDy (optional)

In order to take advantage of latest features you will need to have ProDy library installed.

Windows/Cygwin

Download and install the latest version of Cygwin including appropriate code development packages.
Download, compile, and install the latest version of GROMACS 2016.3 under Cygwin. Follow the standard compilation, installation and testing instructions to build, compile and install GROMACS 2016.3 under Cygwin. For example:

% cd gromacs-2016.3
% mkdir build
% cmake .. -DBUILD_SHARED_LIBS=off -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/cygdrive/c/<YOUR_GROMACS_ROOT>
% make >& make.log
% make install >& make.install.log

Test GROMACS from Cywin command line.
Download and install 64 bit PyMOL 1.8.2.0, which comes with Python 2.7.9.
Test PyMOL.
Update PATH environment variable on Windows to include the following bin directories corresponding to GROMACS and Cygwin:

C:\<YOUR_GROMACS_ROOT>\bin
C:\<YOUR_CYGWIN_PATH>\bin

Install the GROMACS plugin following standard PyMOL instructions. Download latest plugin version from link: https://github.com/makson96/Dynamics/archive/master.zip and unpack it. Run PyMOL. On the top Menu choose Plugin->Manage Plugins->Install... Then choose pymol_plugin_dynamics.py file. After installation restart PyMOL

Latest Snapshots

You can download latest master snapshot by command:

git clone git://github.com/makson96/Dynamics.git

Then run PyMOL as a root. On the top Menu choose Plugin->Manage Plugins->Install... Then choose pymol_plugin_dynamics.py file. After installation restart PyMOL with normal user privilege.

Required dependencies:

PyMOL
GROMACS
ProDy (optional)
PLUMED (optional, compiled into GROMACS)

In order to take advantage of latest features you will need to have ProDy library installed and PLUMED compiled into GROMACS.

References

Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL Tomasz Makarewicz and Rajmund Kaźmierkiewicz Journal of Chemical Information and Modeling 2013 53 (5), 1229-1234
Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis Tomasz Makarewicz, Rajmund Kaźmierkiewicz Journal of Molecular Modeling May 2016, 22:109

License

This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-licenses/GPL-3". Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.
Contributors:
- Tomasz Makarewicz
- Ajit B. Datta
- Sara Boch Kminikowska
- Manish Sud

@@ Line 1: / Line 1: @@
 {{Infobox script-repo
 |type      = plugin
-|download  = https://github.com/tomaszmakarewicz/Dynamics/releases
+|download  = https://github.com/makson96/Dynamics/releases
 |author    = [http://biotech.ug.edu.pl/dzialalnosc_naukowa/zespoly_badawcze/pracownia_symulacji_ukladow_biomolekularnych Laboratory of Biomolecular Systems Simulations]
 |license   = [https://www.gnu.org/licenses/gpl.html GPLv3]
 }}
-[https://github.com/tomaszmakarewicz/Dynamics Dynamics PyMOL Plugin] is plugin for PyMOL, which add molecular dynamics simulation feature. It is meant to be easy to use. The plugin uses GROMACS tools as a back-end. Project is developed as an open source and as such create full open source stack together with PyMOL and GROMACS. Because GROMACS can compile easily only on Unix like systems, the plugin also keep compatibility only with those. No Windows port is expected.
+[https://github.com/makson96/Dynamics Dynamics PyMOL Plugin] is plugin for PyMOL, which add molecular dynamics simulation feature. It is meant to be easy to use. The plugin uses GROMACS tools as a back-end. Project is developed as an open source and as such create full open source stack together with PyMOL and GROMACS. Software works on Linux, MacOS X and Windows/Cygwin.
 == Website ==
-https://github.com/tomaszmakarewicz/Dynamics
+https://github.com/makson96/Dynamics
 == Features ==
@@ Line 23: / Line 23: @@
 * Do your work free of charge and without any restrictions. Feel free to modify any component of the stack.
 * Minimum dependencies. Plugin use the same graphic libraries as PyMOL, so working PyMOL and GROMACS installations are enough to make plugin work.
-Note that exact instruction of how to use program is in the [https://github.com/tomaszmakarewicz/Dynamics/blob/master/manual.odt software manual], which is available together with the plugin.
+Note that exact instruction of how to use program is in the [https://github.com/makson96/Dynamics/blob/master/manual.odt software manual], which is available together with the plugin.
 == Installation ==
-There are at least few ways to install the plugin. In this section we will describe the most common. Please keep in mind, that this plugin is develop for Unix platform - it will not work on MS Windows.
+There are at least few ways to install the plugin. In this section we will describe the most common.
 === Ubuntu ===
 The easiest way to install the plugin is to use PPA repositories:
-  sudo add-apt-repository ppa:tomaszm/dynamics
+  sudo add-apt-repository ppa:makson96/dynamics
   sudo apt-get update
   sudo apt-get install pymol-plugin-dynamics
@@ Line 42: / Line 42: @@
   emerge --ask sci-chemistry/pymol-plugins-dynamics
-=== Other GNU/Linux and Unix===
+=== Other Linux distributions and macOS ===
-The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage:<br>
+The second way for all other platforms, is to download latest release of the plugin directly from its GitHub webpage:<br>
-https://github.com/tomaszmakarewicz/Dynamics/releases <br>
+https://github.com/makson96/Dynamics/releases <br>
-Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''pymol_plugin_dynamics.py''' file. After installation restart PyMOL with normal user privilege.
+Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''pymol_plugin_dynamics.py''' file. After installation restart PyMOL with normal user privilege. On macOS you will need to use [https://pymolwiki.org/index.php/MAC_Install#X11_Hybrid X11 Hybrid] version of the PyMOL.
 Required dependencies:
@@ Line 53: / Line 53: @@
 * ProDy (optional)
 In order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.
+=== Windows/Cygwin ===
+* Download and install the latest version of Cygwin including appropriate code development packages.
+* Download, compile, and install the latest version of GROMACS 2016.3 under Cygwin. Follow the standard compilation, installation and testing instructions to build, compile and install GROMACS 2016.3 under Cygwin. For example:
+ % cd gromacs-2016.3
+ % mkdir build
+ % cmake .. -DBUILD_SHARED_LIBS=off -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/cygdrive/c/<YOUR_GROMACS_ROOT>
+ % make >& make.log
+ % make install >& make.install.log
+* Test GROMACS from Cywin command line.
+* Download and install 64 bit PyMOL 1.8.2.0, which comes with Python 2.7.9.
+* Test PyMOL.
+* Update PATH environment variable on Windows to include the following bin directories corresponding to GROMACS and Cygwin:
+ C:\<YOUR_GROMACS_ROOT>\bin
+ C:\<YOUR_CYGWIN_PATH>\bin
+* Install the GROMACS plugin following standard PyMOL instructions. Download latest plugin version from link: https://github.com/makson96/Dynamics/archive/master.zip and unpack it. Run PyMOL. On the top Menu choose Plugin->Manage Plugins->Install... Then choose pymol_plugin_dynamics.py file. After installation restart PyMOL
 === Latest Snapshots ===
 You can download latest master snapshot by command:
-  git clone git://github.com/tomaszmakarewicz/Dynamics.git
+  git clone git://github.com/makson96/Dynamics.git
 Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''pymol_plugin_dynamics.py''' file. After installation restart PyMOL with normal user privilege.
@@ Line 64: / Line 81: @@
 * GROMACS
 * ProDy (optional)
-In order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.
+* PLUMED (optional, compiled into GROMACS)
+In order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed and [http://www.plumed.org/ PLUMED] compiled into GROMACS.
 == References ==
-[http://pubs.acs.org/doi/abs/10.1021/ci400071x Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL Tomasz Makarewicz and Rajmund Kaźmierkiewicz Journal of Chemical Information and Modeling 2013 53 (5), 1229-1234]
+[http://pubs.acs.org/doi/abs/10.1021/ci400071x Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL Tomasz Makarewicz and Rajmund Kaźmierkiewicz Journal of Chemical Information and Modeling 2013 53 (5), 1229-1234]<br>
+[http://link.springer.com/article/10.1007/s00894-016-2982-4 Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis Tomasz Makarewicz, Rajmund Kaźmierkiewicz Journal of Molecular Modeling May 2016, 22:109]
 == License ==
@@ Line 74: / Line 93: @@
 This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-licenses/GPL-3". Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.<br>
 Contributors:<br>
-- Tomasz Makarewicz (btchtm [at] ug [dot] edu [dot] pl)
+- Tomasz Makarewicz <br>
+- Ajit B. Datta <br>
+- Sara Boch Kminikowska <br>
+- Manish Sud <br>
 [[Category:Plugins]]