Recent changes to GeneralRequirements

Discussion for GeneralRequirements page

Uda Yuma Official — Sun, 27 Feb 2022 20:29:50 -0000

Nada Raja Printing adalah usaha yang bergerak di bidang Penerbitan dan Percetakan. Kami melayani berbagai macam produk layanan jasa terlengkap dan menjadi salah satu pusat Jasa Percetakan Jakarta.

GeneralRequirements modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Mon, 12 Nov 2018 21:01:52 -0000

--- v8
+++ v9
@@ -5,7 +5,7 @@
     [[img src=wrap-good.png alt="Correct wrapping"]]
 * Molecules must not be broken at the periodic boundary box. 
     [[img src=wrap-broken_lipids.png alt="Wrong wrapping - Lipids broken in PBC"]]
-* Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction.
+* Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction. Extremly deformed membranes may lead also to leaflet assignment issues. 
     [[img src=pbc_problems.png alt="Wrong wrapping - Lipids jump over z"]]
 * Connectivity is expected for the whole system. This is  ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the -S_CD order parameter tool. 
     * PDB files can generally _not_ be used as topology files, because connectivity information is  inferred from distances and types only approximately.

GeneralRequirements modified by Toni

Toni — Fri, 20 Dec 2013 13:25:33 -0000

--- v7
+++ v8
@@ -9,6 +9,6 @@
     [[img src=pbc_problems.png alt="Wrong wrapping - Lipids jump over z"]]
 * Connectivity is expected for the whole system. This is  ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the -S_CD order parameter tool. 
     * PDB files can generally _not_ be used as topology files, because connectivity information is  inferred from distances and types only approximately. 
-    * GROMACS users may be able to get .psf files with [this script](http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/).
+    * GROMACS users may be able to Gromacs topology files to .psf files with the [top2psf](http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/) script.

GeneralRequirements modified by Hector Martinez-Seara Monne

Hector Martinez-Seara Monne — Mon, 16 Dec 2013 20:22:17 -0000

--- v6
+++ v7
@@ -2,14 +2,13 @@

 * The membrane's normal must be aligned to Z axis.
 * All tools require that trajectories are wrapped according to periodic boundary conditions. Trajectories can be wrapped at run-time setting the  “Wrap command” (or "-wrapcmd" command line parameter). Wrapping requires periodic box information to be available in the trajectory.  
-    *![Correct wrapping](https://sourceforge.net/p/membplugin/wiki/GeneralRequirements/attachment/wrap-good.png "Correct wrap")
+    [[img src=wrap-good.png alt="Correct wrapping"]]
 * Molecules must not be broken at the periodic boundary box. 
-    *![Wrong wrapping - Lipids broken in PBC](https://sourceforge.net/p/membplugin/wiki/GeneralRequirements/attachment/wrap-broken_lipids.png "Wrong wrapping - Lipids broken in PBC")
+    [[img src=wrap-broken_lipids.png alt="Wrong wrapping - Lipids broken in PBC"]]
 * Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction.
- *![Wrong wrapping - Lipids jump over z](https://sourceforge.net/p/membplugin/wiki/GeneralRequirements/attachment/pbc_problems.png "Wrong wrapping - Lipids jump over z")
+    [[img src=pbc_problems.png alt="Wrong wrapping - Lipids jump over z"]]
 * Connectivity is expected for the whole system. This is  ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the -S_CD order parameter tool. 
     * PDB files can generally _not_ be used as topology files, because connectivity information is  inferred from distances and types only approximately. 
     * GROMACS users may be able to get .psf files with [this script](http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/).

-

GeneralRequirements modified by Hector Martinez-Seara Monne

Hector Martinez-Seara Monne — Mon, 16 Dec 2013 20:10:44 -0000

--- v5
+++ v6
@@ -2,11 +2,14 @@

 * The membrane's normal must be aligned to Z axis.
 * All tools require that trajectories are wrapped according to periodic boundary conditions. Trajectories can be wrapped at run-time setting the  “Wrap command” (or "-wrapcmd" command line parameter). Wrapping requires periodic box information to be available in the trajectory.  
-* Molecules must not be broken at the periodic boundary box.
-* Connectivity is expected for the whole system. This is  ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the S_CD order parameter tool. 
+    *![Correct wrapping](https://sourceforge.net/p/membplugin/wiki/GeneralRequirements/attachment/wrap-good.png "Correct wrap")
+* Molecules must not be broken at the periodic boundary box. 
+    *![Wrong wrapping - Lipids broken in PBC](https://sourceforge.net/p/membplugin/wiki/GeneralRequirements/attachment/wrap-broken_lipids.png "Wrong wrapping - Lipids broken in PBC")
+* Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction.
+ *![Wrong wrapping - Lipids jump over z](https://sourceforge.net/p/membplugin/wiki/GeneralRequirements/attachment/pbc_problems.png "Wrong wrapping - Lipids jump over z")
+* Connectivity is expected for the whole system. This is  ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the -S_CD order parameter tool. 
     * PDB files can generally _not_ be used as topology files, because connectivity information is  inferred from distances and types only approximately. 
     * GROMACS users may be able to get .psf files with [this script](http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/).
-* Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction.
+

-

GeneralRequirements modified by Toni

Toni — Sat, 12 Oct 2013 14:10:33 -0000

--- v4
+++ v5
@@ -6,7 +6,7 @@
 * Connectivity is expected for the whole system. This is  ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the S_CD order parameter tool. 
     * PDB files can generally _not_ be used as topology files, because connectivity information is  inferred from distances and types only approximately. 
     * GROMACS users may be able to get .psf files with [this script](http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/).
-* Assignments of lipids to either leaflet is based on the bilayer's center of mass. Make sure the lipids are properly wrapped in the Z direction.
+* Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction.

GeneralRequirements modified by Toni

Toni — Tue, 08 Oct 2013 10:25:38 -0000

--- v3
+++ v4
@@ -1,7 +1,7 @@
 #General requirements

 * The membrane's normal must be aligned to Z axis.
-* If the trajectory is not pre-wrapped, the  “Wrap command” (or "-wrapcmd" command line parameter) must be set properly. In this case, periodic box information should also be set along the trajectory.  
+* All tools require that trajectories are wrapped according to periodic boundary conditions. Trajectories can be wrapped at run-time setting the  “Wrap command” (or "-wrapcmd" command line parameter). Wrapping requires periodic box information to be available in the trajectory.  
 * Molecules must not be broken at the periodic boundary box.
 * Connectivity is expected for the whole system. This is  ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the S_CD order parameter tool. 
     * PDB files can generally _not_ be used as topology files, because connectivity information is  inferred from distances and types only approximately.

GeneralRequirements modified by Toni

Toni — Tue, 08 Oct 2013 10:23:09 -0000

--- v2
+++ v3
@@ -3,7 +3,7 @@
 * The membrane's normal must be aligned to Z axis.
 * If the trajectory is not pre-wrapped, the  “Wrap command” (or "-wrapcmd" command line parameter) must be set properly. In this case, periodic box information should also be set along the trajectory.  
 * Molecules must not be broken at the periodic boundary box.
-* Connectivity is expected for the whole system. This is usually ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the S_CD order parameter tool. 
+* Connectivity is expected for the whole system. This is  ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the S_CD order parameter tool. 
     * PDB files can generally _not_ be used as topology files, because connectivity information is  inferred from distances and types only approximately. 
     * GROMACS users may be able to get .psf files with [this script](http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/).
 * Assignments of lipids to either leaflet is based on the bilayer's center of mass. Make sure the lipids are properly wrapped in the Z direction.

GeneralRequirements modified by Toni

Toni — Tue, 08 Oct 2013 10:22:35 -0000

--- v1
+++ v2
@@ -1,6 +1,12 @@
 #General requirements

-* In order to get reproducible results, it is recommended that the membrane is aligned to Z axis.
-* If you want results for only one leaflet, the trajectory must be wrapped in the Z axis as this is needed to determine membrane leaflets properly, and lipid resnames must be set properly (see [GUIMainwindow]),
-* In this case, trajectory file must contain simulation box dimensions, and system must be wrapped into one periodic boundary cell (pbc). This can be achieved by setting properly the “Wrap command” in main window or the command line argument (-wrapcmd). Trajectories where molecules are split (i. e. GROMACS) must be preprocessed in order to join broken residues together.
-* If wrap is not needed, you can empty the “Wrap command” in main window, or set the "-wrapcmd" command line argument to "{}".
+* The membrane's normal must be aligned to Z axis.
+* If the trajectory is not pre-wrapped, the  “Wrap command” (or "-wrapcmd" command line parameter) must be set properly. In this case, periodic box information should also be set along the trajectory.  
+* Molecules must not be broken at the periodic boundary box.
+* Connectivity is expected for the whole system. This is usually ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the S_CD order parameter tool. 
+    * PDB files can generally _not_ be used as topology files, because connectivity information is  inferred from distances and types only approximately. 
+    * GROMACS users may be able to get .psf files with [this script](http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/).
+* Assignments of lipids to either leaflet is based on the bilayer's center of mass. Make sure the lipids are properly wrapped in the Z direction.
+ 
+
+

GeneralRequirements modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Tue, 08 Oct 2013 09:23:15 -0000

General requirements

In order to get reproducible results, it is recommended that the membrane is aligned to Z axis.
If you want results for only one leaflet, the trajectory must be wrapped in the Z axis as this is needed to determine membrane leaflets properly, and lipid resnames must be set properly (see [GUIMainwindow]),
In this case, trajectory file must contain simulation box dimensions, and system must be wrapped into one periodic boundary cell (pbc). This can be achieved by setting properly the “Wrap command” in main window or the command line argument (-wrapcmd). Trajectories where molecules are split (i. e. GROMACS) must be preprocessed in order to join broken residues together.
If wrap is not needed, you can empty the “Wrap command” in main window, or set the "-wrapcmd" command line argument to "{}".