Recent changes to Home

Home modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Thu, 14 Jun 2018 18:47:33 -0000

--- v42
+++ v43
@@ -47,7 +47,7 @@
 The documents are distributed together with the simulation data necessary to fully reproduce the analysis.

-### Command-line interface
+### Command-line interface  

 All of the tools' functions can be accessed from VMD's scripting environment. The easiest way to learn about the syntax is to keep an eye on the console, where the equivalent TCL command is printed upon any calculation.

Home modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Thu, 14 Jun 2018 18:35:39 -0000

--- v41
+++ v42
@@ -53,6 +53,14 @@

 If you are in text-only mode, you might need to load mempluguin package first with 'package require membplugin'.

+Run the following commands for usage info:
+
+membranescd
+lipidarea
+interdigitation
+lipidtilt
+membranethickness
+

 ### Citation

Home modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Thu, 14 Jun 2018 18:14:48 -0000

--- v40
+++ v41
@@ -51,6 +51,8 @@

 All of the tools' functions can be accessed from VMD's scripting environment. The easiest way to learn about the syntax is to keep an eye on the console, where the equivalent TCL command is printed upon any calculation.

+If you are in text-only mode, you might need to load mempluguin package first with 'package require membplugin'.
+

 ### Citation

Home modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Wed, 23 Jul 2014 11:40:08 -0000

--- v39
+++ v40
@@ -56,7 +56,7 @@

 The plugin is described in the Bioinformatics paper _MEMBPLUGIN: studying membrane complexity in VMD_, which you should cite if you use this software in publications.

-> R. Guixà-González; I. Rodríguez-Espigares; J. M. Ramírez-Anguita; P. Carrió-Gaspar; H. Martinez-Seara; T. Giorgino; J. Selent. _MEMBPLUGIN: studying membrane complexity in VMD_.  Bioinformatics 2014; [doi:10.1093/bioinformatics/btu037](http://dx.doi.org/10.1093/bioinformatics/btu037)
+> R. Guixà-González; I. Rodríguez-Espigares; J. M. Ramírez-Anguita; P. Carrió-Gaspar; H. Martinez-Seara; T. Giorgino; J. Selent. _MEMBPLUGIN: studying membrane complexity in VMD_.  Bioinformatics 2014; vol. 30 (10) p. 1478-1480  [doi:10.1093/bioinformatics/btu037](http://dx.doi.org/10.1093/bioinformatics/btu037)

 ### License

Home modified by Ramon Guixa

Ramon Guixa — Thu, 23 Jan 2014 11:37:50 -0000

--- v38
+++ v39
@@ -56,7 +56,7 @@

 The plugin is described in the Bioinformatics paper _MEMBPLUGIN: studying membrane complexity in VMD_, which you should cite if you use this software in publications.

-> R. Guixa-Gonzalez; I. Rodriguez-Espigares; J. M. Ramirez-Anguita; P. Carrio-Gaspar; H. Martinez-Seara; T. Giorgino; J. Selent. _MEMBPLUGIN: studying membrane complexity in VMD_.  Bioinformatics 2014; [doi:10.1093/bioinformatics/btu037](http://dx.doi.org/10.1093/bioinformatics/btu037)
+> R. Guixà-González; I. Rodríguez-Espigares; J. M. Ramírez-Anguita; P. Carrió-Gaspar; H. Martinez-Seara; T. Giorgino; J. Selent. _MEMBPLUGIN: studying membrane complexity in VMD_.  Bioinformatics 2014; [doi:10.1093/bioinformatics/btu037](http://dx.doi.org/10.1093/bioinformatics/btu037)

 ### License

Home modified by Toni

Toni — Thu, 23 Jan 2014 08:26:06 -0000

--- v37
+++ v38
@@ -56,7 +56,7 @@

 The plugin is described in the Bioinformatics paper _MEMBPLUGIN: studying membrane complexity in VMD_, which you should cite if you use this software in publications.

-> Ramon Guixa-Gonzalez; Ismael Rodriguez-Espigares; Juan Manuel Ramirez-Anguita; Pau Carrio-Gaspar; Hector Martinez-Seara; Toni Giorgino; Jana Selent. _MEMBPLUGIN: studying membrane complexity in VMD_.  Bioinformatics 2014; [doi:10.1093/bioinformatics/btu037](http://dx.doi.org/10.1093/bioinformatics/btu037)
+> R. Guixa-Gonzalez; I. Rodriguez-Espigares; J. M. Ramirez-Anguita; P. Carrio-Gaspar; H. Martinez-Seara; T. Giorgino; J. Selent. _MEMBPLUGIN: studying membrane complexity in VMD_.  Bioinformatics 2014; [doi:10.1093/bioinformatics/btu037](http://dx.doi.org/10.1093/bioinformatics/btu037)

 ### License

Home modified by Toni

Toni — Thu, 23 Jan 2014 08:25:22 -0000

--- v36
+++ v37
@@ -54,7 +54,9 @@

 ### Citation 

-The plugin is described in the  paper _MEMBPLUGIN: studying membrane complexity in VMD_, which you should cite if you use this software in publications.
+The plugin is described in the Bioinformatics paper _MEMBPLUGIN: studying membrane complexity in VMD_, which you should cite if you use this software in publications.
+
+> Ramon Guixa-Gonzalez; Ismael Rodriguez-Espigares; Juan Manuel Ramirez-Anguita; Pau Carrio-Gaspar; Hector Martinez-Seara; Toni Giorgino; Jana Selent. _MEMBPLUGIN: studying membrane complexity in VMD_.  Bioinformatics 2014; [doi:10.1093/bioinformatics/btu037](http://dx.doi.org/10.1093/bioinformatics/btu037)

 ### License

Home modified by Toni

Toni — Sat, 04 Jan 2014 09:59:21 -0000

--- v35
+++ v36
@@ -1,8 +1,8 @@
 # MEMBPLUGIN
 ##### Studying membrane complexity in VMD

+MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers.

-MEMBPLUGIN is a collection of visual and command-line tools that run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers.

 ### Installation

Home modified by Toni

Toni — Sat, 21 Dec 2013 21:54:44 -0000

--- v34
+++ v35
@@ -37,7 +37,7 @@

-### Use cases
+### Tutorial and case study

 Two extended write-ups show the use of MEMBPLUGIN on realistic systems: 

@@ -52,7 +52,7 @@
 All of the tools' functions can be accessed from VMD's scripting environment. The easiest way to learn about the syntax is to keep an eye on the console, where the equivalent TCL command is printed upon any calculation.

-### Citation
+### Citation 

 The plugin is described in the  paper _MEMBPLUGIN: studying membrane complexity in VMD_, which you should cite if you use this software in publications.

Home modified by Toni

Toni — Fri, 20 Dec 2013 13:23:53 -0000

--- v33
+++ v34
@@ -21,15 +21,6 @@
 Where __atom selections__ are required, VMD's atom selection syntax applies. Additionally, the _membplugin_lipids_ macro is available to indicate the residue names listed in the configuration, notably those supported by the [CHARMM-GUI](http://www.charmm-gui.org/) membrane builder.

-### Use cases
-
-Two extended write-ups show the use of MEMBPLUGIN on realistic systems: 
-
-1.  a [step-by-step tutorial](https://sourceforge.net/projects/membplugin/files/Tutorial/), suitable for beginners or first-time users; and 
-1.  an advanced [case study](https://sourceforge.net/projects/membplugin/files/Case%20Study/), showing the analysis performed on cholesterol-enriched membranes.
-
-The documents are distributed together with the simulation data necessary to fully reproduce the analysis.
-

 ### Tools included 

@@ -45,6 +36,17 @@
 Additionally, links are provided for the external _[Diffusion Coefficient](http://multiscalelab.org/utilities/DiffusionCoefficientTool)_ and _[Density Profile](http://multiscalelab.org/utilities/DensityProfileTool)_ tools.

+
+### Use cases
+
+Two extended write-ups show the use of MEMBPLUGIN on realistic systems: 
+
+1.  a [step-by-step tutorial](https://sourceforge.net/projects/membplugin/files/Tutorial/), suitable for beginners or first-time users; and 
+1.  an advanced [case study](https://sourceforge.net/projects/membplugin/files/Case%20Study/), showing the analysis performed on cholesterol-enriched membranes.
+
+The documents are distributed together with the simulation data necessary to fully reproduce the analysis.
+
+
 ### Command-line interface

 All of the tools' functions can be accessed from VMD's scripting environment. The easiest way to learn about the syntax is to keep an eye on the console, where the equivalent TCL command is printed upon any calculation.