Recent changes to FAQ_running

FAQ_running modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:31:03 -0000

--- v10
+++ v11
@@ -1,4 +1,4 @@
-Frequently asked questions at running the ermod program
+Frequently asked questions at running the erdst program
 ====

 ###Program fails to run with an error message: "Error: cannot find plugin paths, please set ERMOD_PLUGINS environment variable"###
@@ -71,6 +71,8 @@

 ###Ermod cannot read HISTORY file if it is linked to another symbolic link###

+In version 1.0, this bug should have been fixed. If you encounter this bug please report to devs (at ermod-users mailing list or directly mail us).
+
 If the HISTORY file is symlinked to ../otherdir/foo and ../otherdir/foo is further symlinked to foo2, then the program searches for foo2 in the current directory instead of ../otherdir.
 This is a feature of VMD plugin-based file I/O and cannot be fixed at the moment.
 A current workaround is to link the target with the *absolute* path.

FAQ_running modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 24 Jul 2015 09:02:10 -0000

--- v9
+++ v10
@@ -79,4 +79,4 @@

 The extension of the trajectory file must match ".nc" for ERmod to recognize the file as the netCDF format. Rename the trajectory file to have .nc extension.

-In version 0.3, development version, user can use "ERMOD_FORCE_PLUGIN_TYPE" environment variable to force the plugin type. For example, in sh/bash/zsh, "export ERMOD_FORCE_PLUGIN_TYPE=nc" forces ERmod to use netCDF plugin to read ALL trajectories. 
+In version 0.3, user can use "ERMOD_FORCE_PLUGIN_TYPE" environment variable to force the plugin type. For example, in sh/bash/zsh, "export ERMOD_FORCE_PLUGIN_TYPE=nc" forces ERmod to use netCDF plugin to read ALL trajectories.

FAQ_running modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 08 May 2015 05:53:12 -0000

--- v8
+++ v9
@@ -40,7 +40,7 @@
 The energy should be chosen so that it is small enough.
 A general guideline is that for an ion of total charge of +/-1, --minenergy -80 will be a good starting point.
 When the charge is +/-2, --minenergy -120 will be a good starting point.
-For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03).
+For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameter files for ermod](parameters-ermod03).

 User **must** specify the same *energy* meshes for **both** `soln` and `refs` parts.

FAQ_running modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 07 Aug 2014 03:18:28 -0000

--- v7
+++ v8
@@ -15,14 +15,14 @@

 ~~~~
 ::::sh
-export ERMOD_PLUGINS=(/path/to/ermod-source)/vmdplugins/libexec
+export ERMOD_PLUGINS=(path to the ERmod source-code directory)/vmdplugins/libexec
 ~~~~

 If you are using csh or tcsh,

 ~~~~
 ::::csh
-setenv ERMOD_PLUGINS (/path/to/ermod-source)/vmdplugins/libexec
+setenv ERMOD_PLUGINS (path to the ERmod source-code directory)/vmdplugins/libexec
 ~~~~

 The command should be executed every time before you execute ermod.

FAQ_running modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 31 Oct 2013 01:33:16 -0000

--- v6
+++ v7
@@ -40,7 +40,7 @@
 The energy should be chosen so that it is small enough.
 A general guideline is that for an ion of total charge of +/-1, --minenergy -80 will be a good starting point.
 When the charge is +/-2, --minenergy -120 will be a good starting point.
-For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameters for ermod](parameters-ermod)).
+For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03).

 User **must** specify the same *energy* meshes for **both** `soln` and `refs` parts.

FAQ_running modified by Shun Sakuraba

Shun Sakuraba — Sun, 02 Jun 2013 10:09:03 -0000

--- v5
+++ v6
@@ -80,5 +80,3 @@
 The extension of the trajectory file must match ".nc" for ERmod to recognize the file as the netCDF format. Rename the trajectory file to have .nc extension.

 In version 0.3, development version, user can use "ERMOD_FORCE_PLUGIN_TYPE" environment variable to force the plugin type. For example, in sh/bash/zsh, "export ERMOD_FORCE_PLUGIN_TYPE=nc" forces ERmod to use netCDF plugin to read ALL trajectories. 
-
-[1] http://www.ks.uiuc.edu/Development/MDTools/catdcd/

FAQ_running modified by Shun Sakuraba

Shun Sakuraba — Sun, 02 Jun 2013 10:08:36 -0000

--- v4
+++ v5
@@ -74,3 +74,11 @@
 If the HISTORY file is symlinked to ../otherdir/foo and ../otherdir/foo is further symlinked to foo2, then the program searches for foo2 in the current directory instead of ../otherdir.
 This is a feature of VMD plugin-based file I/O and cannot be fixed at the moment.
 A current workaround is to link the target with the *absolute* path.
+
+###ERmod cannot read netCDF trejectory.###
+
+The extension of the trajectory file must match ".nc" for ERmod to recognize the file as the netCDF format. Rename the trajectory file to have .nc extension.
+
+In version 0.3, development version, user can use "ERMOD_FORCE_PLUGIN_TYPE" environment variable to force the plugin type. For example, in sh/bash/zsh, "export ERMOD_FORCE_PLUGIN_TYPE=nc" forces ERmod to use netCDF plugin to read ALL trajectories. 
+
+[1] http://www.ks.uiuc.edu/Development/MDTools/catdcd/

WikiPage FAQ_running modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Wed, 02 May 2012 15:21:55 -0000

--- v3 
+++ v4 
@@ -71,6 +71,6 @@
 
 ###Ermod cannot read HISTORY file if it is linked to another symbolic link###
 
-If the HISTORY file is symlinked to ../otherdir/foo and ../otherdir/foo is further symlinked to foo2, then program searches for foo2 in the current directory instead of ../otherdir.
+If the HISTORY file is symlinked to ../otherdir/foo and ../otherdir/foo is further symlinked to foo2, then the program searches for foo2 in the current directory instead of ../otherdir.
 This is a feature of VMD plugin-based file I/O and cannot be fixed at the moment.
 A current workaround is to link the target with the *absolute* path.

WikiPage FAQ_running modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Wed, 02 May 2012 15:09:01 -0000

--- v2 
+++ v3 
@@ -73,4 +73,4 @@
 
 If the HISTORY file is symlinked to ../otherdir/foo and ../otherdir/foo is further symlinked to foo2, then program searches for foo2 in the current directory instead of ../otherdir.
 This is a feature of VMD plugin-based file I/O and cannot be fixed at the moment.
-A current work-around is to link the target with the *absolute* path.
+A current workaround is to link the target with the *absolute* path.

WikiPage FAQ_running modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Wed, 02 May 2012 12:13:57 -0000

--- v1 
+++ v2 
@@ -71,5 +71,6 @@
 
 ###Ermod cannot read HISTORY file if it is linked to another symbolic link###
 
+If the HISTORY file is symlinked to ../otherdir/foo and ../otherdir/foo is further symlinked to foo2, then program searches for foo2 in the current directory instead of ../otherdir.
 This is a feature of VMD plugin-based file I/O and cannot be fixed at the moment.
 A current work-around is to link the target with the *absolute* path.