GROMACS Plugin - Revision history

Cchem: 2 revisions

2017-11-13T03:27:08Z

2 revisions

TomaszMakarewicz: Update launchpad links

2017-10-25T10:43:36Z

Update launchpad links

TomaszMakarewicz: Update GitHub links

2017-10-25T09:54:03Z

Update GitHub links

Cchem: 1 revision

2017-07-24T02:39:11Z

1 revision

TomaszMakarewicz at 09:12, 4 July 2017

2017-07-04T09:12:02Z

Cchem: 1 revision

2017-06-26T04:31:24Z

1 revision

TomaszMakarewicz: Add windows instructions

2017-05-31T12:03:43Z

Add windows instructions

Cchem: 2 revisions

2016-05-31T05:42:48Z

2 revisions

TomaszMakarewicz at 12:58, 4 May 2016

2016-05-04T12:58:08Z

TomaszMakarewicz: Update

2016-05-04T12:57:06Z

Update

@@ Line 32: / Line 32: @@
 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 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. Software works on Linux, MacOS X and Windows/Cygwin.
+[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 ==
@@ Line 45: / Line 45: @@
 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. On macOS you will need to use [https://pymolwiki.org/index.php/MAC_Install#X11_Hybrid X11 Hybrid] version of the PyMOL.
@@ Line 69: / Line 69: @@
   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
+* 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 93: / 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) <br>
+- Tomasz Makarewicz <br>
 - Ajit B. Datta <br>
 - Sara Boch Kminikowska <br>

@@ Line 42: / Line 42: @@
   emerge --ask sci-chemistry/pymol-plugins-dynamics
-=== Other Linux distributions and MacOS X ===
+=== 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>
-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 6: / Line 6: @@
 }}
-[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/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 ==
@@ Line 27: / Line 27: @@
 == 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 ===
@@ Line 42: / Line 42: @@
   emerge --ask sci-chemistry/pymol-plugins-dynamics
-=== Other GNU/Linux and Unix===
+=== 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:<br>
@@ 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.
 === Latest Snapshots ===
@@ Line 76: / 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 (btchtm [at] ug [dot] edu [dot] pl) <br>
 [[Category:Plugins]]

@@ Line 69: / Line 69: @@
 == 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]

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