PyMOL Wiki - User contributions [en]

GROMACS Plugin

2017-10-25T10:43:36Z

TomaszMakarewicz: Update launchpad links

{{Infobox script-repo
|type = plugin
|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/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/makson96/Dynamics

== Features ==

[[File:Menu1.png | 600px]]

* 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 [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.

=== 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 [http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-dynamics?arches=all 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 [https://pymolwiki.org/index.php/MAC_Install#X11_Hybrid 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 [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/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 [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://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 ==

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 

[[Category:Plugins]]

GROMACS Plugin

2017-10-25T09:54:03Z

TomaszMakarewicz: Update GitHub links

{{Infobox script-repo
|type = plugin
|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/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/makson96/Dynamics

== Features ==

[[File:Menu1.png | 600px]]

* 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 [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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/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 [http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-dynamics?arches=all 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 [https://pymolwiki.org/index.php/MAC_Install#X11_Hybrid 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 [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/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 [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://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 ==

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 

[[Category:Plugins]]

GROMACS Plugin

2017-07-04T09:12:02Z

TomaszMakarewicz:

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/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. Software works on Linux, MacOS X and Windows/Cygwin.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Menu1.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/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 [http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-dynamics?arches=all 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/tomaszmakarewicz/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 [https://pymolwiki.org/index.php/MAC_Install#X11_Hybrid 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 [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/tomaszmakarewicz/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
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 [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://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 ==

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 (btchtm [at] ug [dot] edu [dot] pl) 
- Ajit B. Datta 
- Sara Boch Kminikowska 
- Manish Sud 

[[Category:Plugins]]

GROMACS Plugin

2017-05-31T12:03:43Z

TomaszMakarewicz: Add windows instructions

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/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. Software works on Linux, MacOS X and Windows/Cygwin.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Menu1.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/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 [http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-dynamics?arches=all Gentoo ebuild system]. To make the installation use (as root):
emerge --ask sci-chemistry/pymol-plugins-dynamics

=== Other Linux distributions and MacOS X ===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/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.

Required dependencies:
* PyMOL
* 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.

=== 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/tomaszmakarewicz/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
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 [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://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 ==

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 (btchtm [at] ug [dot] edu [dot] pl) 
- Ajit B. Datta 
- Sara Boch Kminikowska 
- Manish Sud 

[[Category:Plugins]]

GROMACS Plugin

2016-05-04T12:58:08Z

TomaszMakarewicz:

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Menu1.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/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 [http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-dynamics?arches=all Gentoo ebuild system]. To make the installation use (as root):
emerge --ask sci-chemistry/pymol-plugins-dynamics

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/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.

Required dependencies:
* PyMOL
* 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.

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/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 [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://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 ==

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 (btchtm [at] ug [dot] edu [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2016-05-04T12:57:06Z

TomaszMakarewicz: Update

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Menu1.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/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 [http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-dynamics?arches=all Gentoo ebuild system]. To make the installation use (as root):
emerge --ask sci-chemistry/pymol-plugins-dynamics

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/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.

Required dependencies:
* PyMOL
* 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.

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/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 [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://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 ==

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 (btchtm [at] ug [dot] edu [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2015-03-10T10:31:35Z

TomaszMakarewicz: /* Gentoo */

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Menu1.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/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 [http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-dynamics?arches=all Gentoo ebuild system]. To make the installation use (as root):
emerge --ask sci-chemistry/pymol-plugins-dynamics

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/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.

Required dependencies:
* PyMOL
* 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.

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/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)
In order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.

== 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]

== 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 (btchtm [at] ug [dot] edu [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2015-03-10T10:31:04Z

TomaszMakarewicz: Add Gentoo

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Menu1.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/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 [http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-dynamics?arches=all Gentoo ebuild system]. To make the installation use:
root #emerge --ask sci-chemistry/pymol-plugins-dynamics

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/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.

Required dependencies:
* PyMOL
* 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.

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/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)
In order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.

== 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]

== 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 (btchtm [at] ug [dot] edu [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2015-03-10T09:59:59Z

TomaszMakarewicz:

GROMACS Plugin

2015-03-10T09:43:56Z

TomaszMakarewicz:

File:Menu1.png

2015-03-10T09:43:19Z

TomaszMakarewicz: Dynamics PyMOL Plugin Menu 2.0

Dynamics PyMOL Plugin Menu 2.0

GROMACS Plugin

2015-03-10T09:41:09Z

TomaszMakarewicz:

GROMACS Plugin

2014-01-21T10:24:10Z

TomaszMakarewicz: correct domain name

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/Dynamics/releases
|author = [http://www.biotech.ug.edu.pl/index_eng.php?mmenu=10121&katedra=5&zaklad=2 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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Figure2a.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/dynamics
sudo apt-get update
sudo apt-get install dynamics-pymol-plugin
All required libraries will be downloaded as dependencies. Supported versions of Ubuntu are latest stable and latest LTS.

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/Dynamics/releases 
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* Tix

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/Dynamics.git
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* ProDy
Note that latest snapshot do not require Tix anymore. But in order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.

== 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]

== 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 (btchtm [at] ug [dot] edu [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2013-08-27T13:28:13Z

TomaszMakarewicz: Update email

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/Dynamics/releases
|author = [http://www.biotech.ug.gda.pl/index_eng.php?mmenu=10121&katedra=5&zaklad=2 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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Figure2a.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/dynamics
sudo apt-get update
sudo apt-get install dynamics-pymol-plugin
All required libraries will be downloaded as dependencies. Supported versions of Ubuntu are latest stable and latest LTS.

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/Dynamics/releases 
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* Tix

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/Dynamics.git
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* ProDy
Note that latest snapshot do not require Tix anymore. But in order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.

== 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]

== 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 (btchtm [at] ug [dot] gda [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2013-07-29T14:04:58Z

TomaszMakarewicz: Typo fixes

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/Dynamics/releases
|author = [http://www.biotech.ug.gda.pl/index_eng.php?mmenu=10121&katedra=5&zaklad=2 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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Features ==

[[File:Figure2a.png | 600px]]

* 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 [https://github.com/tomaszmakarewicz/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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/dynamics
sudo apt-get update
sudo apt-get install dynamics-pymol-plugin
All required libraries will be downloaded as dependencies. Supported versions of Ubuntu are latest stable and latest LTS.

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/Dynamics/releases 
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* Tix

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/Dynamics.git
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* ProDy
Note that latest snapshot do not require Tix anymore. But in order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.

== 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]

== 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 (tomaszm [at] biotech [dot] ug [dot] edu [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2013-07-29T12:39:30Z

TomaszMakarewicz: Add Features list

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/Dynamics/releases
|author = [http://www.biotech.ug.gda.pl/index_eng.php?mmenu=10121&katedra=5&zaklad=2 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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Feauters ==

[[File:Figure2a.png | 600px]]

* 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 modyfie 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.

== 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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/dynamics
sudo apt-get update
sudo apt-get install dynamics-pymol-plugin
All required libraries will be downloaded as dependencies. Supported versions of Ubuntu are latest stable and latest LTS.

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well, is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/Dynamics/releases 
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* Tix

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/Dynamics.git
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* ProDy
Note that latest snapshot do not require Tix anymore. But in order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.

== 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]

== 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 (tomaszm [at] biotech [dot] ug [dot] edu [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2013-07-29T12:26:55Z

TomaszMakarewicz: Further improvements

{{Infobox script-repo
|type = plugin
|download = https://github.com/tomaszmakarewicz/Dynamics/releases
|author = [http://www.biotech.ug.gda.pl/index_eng.php?mmenu=10121&katedra=5&zaklad=2 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.

== Website ==

https://github.com/tomaszmakarewicz/Dynamics

== Feauters ==

[[File:Figure2a.png | 600px]]

* aa
* bb
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.

== 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.

=== Ubuntu ===

The easiest way to install the plugin is to use PPA repositories:
sudo add-apt-repository ppa:tomaszm/dynamics
sudo apt-get update
sudo apt-get install dynamics-pymol-plugin
All required libraries will be downloaded as dependencies. Supported versions of Ubuntu are latest stable and latest LTS.

=== Other GNU/Linux and Unix===

The second way for all other platforms or Ubuntu as well is to download latest release of the plugin directly from its GitHub webpage: 
https://github.com/tomaszmakarewicz/Dynamics/releases 
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* Tix

=== Latest Snapshots ===

You can download latest master snapshot by command:
git clone git://github.com/tomaszmakarewicz/Dynamics.git
Then run PyMOL as a root. On the top Menu choose '''Plugin->Manage Plugins->Install...''' Then choose '''dynamics_pymol_plugin.py''' file. After installation restart PyMOL with normal user privilege.

Required dependencies:
* PyMOL
* GROMACS
* ProDy
Note that latest snapshot do not require Tix anymore. But in order to take advantage of latest features you will need to have [http://www.csb.pitt.edu/prody/ ProDy] library installed.

== 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]

== 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 (tomaszm [at] biotech [dot] ug [dot] edu [dot] pl)

[[Category:Plugins]]

GROMACS Plugin

2013-07-29T12:06:50Z

TomaszMakarewicz: Initial webpage.

File:Figure2a.png

2013-07-29T11:57:13Z

TomaszMakarewicz: Main Window in Dynamics PyMOL Plugin

Main Window in Dynamics PyMOL Plugin