Recent changes to LongRangeCorrectionLJ

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sun, 04 Sep 2016 14:46:32 -0000

--- v10
+++ v11
@@ -3,18 +3,18 @@

 The long-range correction of the Lennard-Jones interaction between the solute and solvent can be computed in ERmod.
 To enable this computation, it is enough to set ljlrc = 'yes' in parameters_fe as of ver 0.3.5
-and it is necessary to follow the procedures described at the end of this page when the version is 0.3.4 or earlier.
+and it is necessary to follow the procedures described below in this page when the version is 0.3.4 or earlier.

 When ljlrc = 'yes' is set in parameters_fe, it is also necessary to set the average volume of the system to avevolume.
-It does not affect the result whether the avevolume value is taken from the reference solvent or from solution.
+When the system is large enough, it has only a negligible effect on the computed result whether the avevolume value is taken from the reference solvent or from solution.
 parameters_fe is then read, for example, as

 ~~~~
 ::::sh
-   ....
+  ....
  ljlrc = 'yes'
  avevolume = 0.14752840E+05
-   ....
+  ....
 ~~~~

 The unit of avevolume is Angstrom^3; note that it not be given in nm^3.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sun, 04 Sep 2016 08:32:52 -0000

--- v9
+++ v10
@@ -5,16 +5,16 @@
 To enable this computation, it is enough to set ljlrc = 'yes' in parameters_fe as of ver 0.3.5
 and it is necessary to follow the procedures described at the end of this page when the version is 0.3.4 or earlier.

-When ljlrc = 'yes' set in parameters_fe, it is also necessary to set the average volume of the system to avevolume.
+When ljlrc = 'yes' is set in parameters_fe, it is also necessary to set the average volume of the system to avevolume.
 It does not affect the result whether the avevolume value is taken from the reference solvent or from solution.
 parameters_fe is then read, for example, as

 ~~~~
 ::::sh
-      ....
+   ....
  ljlrc = 'yes'
  avevolume = 0.14752840E+05
-      ....
+   ....
 ~~~~

 The unit of avevolume is Angstrom^3; note that it not be given in nm^3.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sun, 04 Sep 2016 08:32:28 -0000

--- v8
+++ v9
@@ -5,16 +5,20 @@
 To enable this computation, it is enough to set ljlrc = 'yes' in parameters_fe as of ver 0.3.5
 and it is necessary to follow the procedures described at the end of this page when the version is 0.3.4 or earlier.

-By setting ljlrc = 'yes' in parameters_fe, user is required to prepare a file contaning the average volume of the reference solvent, which is read, for example, as
+When ljlrc = 'yes' set in parameters_fe, it is also necessary to set the average volume of the system to avevolume.
+It does not affect the result whether the avevolume value is taken from the reference solvent or from solution.
+parameters_fe is then read, for example, as

 ~~~~
 ::::sh
-cat volumedata
-30106.4
+      ....
+ ljlrc = 'yes'
+ avevolume = 0.14752840E+05
+      ....
 ~~~~

-The volumedata file simpy has the average volume of the reference solvent in Angstrom^3 unit; note that it not be given in nm^3.
-If the volumedata file is not present, user is asked
+The unit of avevolume is Angstrom^3; note that it not be given in nm^3.
+When avevolume is not set in parameters_fe, user is asked

 ~~~~
 ::::sh
@@ -42,3 +46,20 @@

 Without stating ljlrc = 'yes' in parameters_fe, the modified slvfe works just as in the same way as the original slvfe.
 The difference between the original and modified slvfe.F90 is written in the diff_slvfe file in the extensions/LJLRC directory.
+By setting ljlrc = 'yes' in parameters_fe, user is required to prepare a volumedata file which contains the average volume of the system.
+volumedata is read, for example, as
+
+~~~~
+::::sh
+cat volumedata
+30106.4
+~~~~
+
+If the volumedata file is not present, user is asked
+
+~~~~
+::::sh
+  What is the average volume of reference solvent? (in Angstrom^3)
+~~~~
+
+and is to type the average volume in Angstrom^3 directly on terminal.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sun, 28 Aug 2016 03:43:11 -0000

--- v7
+++ v8
@@ -23,8 +23,7 @@

 and is to type the average volume in Angstrom^3 directly on terminal.

-**Caution**: The Lennard-Jones long-range correction scheme can be used only when the solvent distribution is homogeneous (radial distribution function is essentially unity) when the solvent molecule is separated beyond the Lennard-Jones cutoff distance in any direction from any atom in the solute molecule. The correction scheme may not be applied when the solute and/or solvent molecule is comparable in size to
-or larger than the cutoff radius, which is typically ~10 Angstrom, or when the solvent is inhomogeneous in nanoscale and, for example, is micelle or lipid membrane.
+**Caution**: The Lennard-Jones long-range correction scheme can be used only when the solvent distribution is homogeneous (radial distribution function is essentially unity) when the solvent molecule is separated beyond the Lennard-Jones cutoff distance in any direction from any atom in the solute molecule. The correction scheme may not be applied when the solute and/or solvent molecule is comparable in size to or larger than the cutoff radius, which is typically ~10 Angstrom, or when the solvent is inhomogeneous in nanoscale and, for example, is micelle or lipid membrane.

 When the version of ERmod is 0.3.4 or earlier, the following procedures are necessary.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 26 Aug 2016 08:04:05 -0000

--- v6
+++ v7
@@ -29,9 +29,9 @@

 When the version of ERmod is 0.3.4 or earlier, the following procedures are necessary.
 In the parent directory of the distributed ERmod package, there is a sub-directory extensions/LJLRC.
-The modifed slvfe.F90 program contained in this sub-directory can evaluate the long-range correction.
-The slvfe.F90 program contained in the extensions/LJLRC directory has a key of ljlrc, which enables the Lennard-Jones long-range correction at ljlrc = 'yes'.
-To use the slvfe.F90 program contained in this directory, user simply does the followings in the parent directory of ERmod.
+The modifed slvfe.F90 program contained in this sub-directory can evaluate the long-range correction.
+The slvfe.F90 program contained in the extensions/LJLRC directory has a key of ljlrc, which enables the Lennard-Jones long-range correction at ljlrc = 'yes'.
+To use the slvfe.F90 program contained in this directory, user simply does the followings in the parent directory of ERmod.

 ~~~~
 ::::sh
@@ -42,4 +42,4 @@
 ~~~~

 Without stating ljlrc = 'yes' in parameters_fe, the modified slvfe works just as in the same way as the original slvfe.
-The difference between the original and modified slvfe.F90 is written in the diff_slvfe file in the extensions/LJLRC directory.
+The difference between the original and modified slvfe.F90 is written in the diff_slvfe file in the extensions/LJLRC directory.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 26 Aug 2016 08:03:06 -0000

--- v5
+++ v6
@@ -28,8 +28,8 @@

 When the version of ERmod is 0.3.4 or earlier, the following procedures are necessary.
-In the parent directory of the distributed ERmod package, there is a sub-directory extensions/LJLRC.
-The modifed slvfe.F90 program contained in that sub-directory can evaluate the long-range correction.
+In the parent directory of the distributed ERmod package, there is a sub-directory extensions/LJLRC.
+The modifed slvfe.F90 program contained in this sub-directory can evaluate the long-range correction.
 The slvfe.F90 program contained in the extensions/LJLRC directory has a key of ljlrc, which enables the Lennard-Jones long-range correction at ljlrc = 'yes'.
 To use the slvfe.F90 program contained in this directory, user simply does the followings in the parent directory of ERmod.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 26 Aug 2016 08:02:22 -0000

--- v4
+++ v5
@@ -23,8 +23,7 @@

 and is to type the average volume in Angstrom^3 directly on terminal.

-**Caution**: The Lennard-Jones long-range correction scheme can be used only when the solvent distribution is homogeneous (radial distribution function is essentially unity) when the solvent molecule is separated beyond the Lennard-Jones cutoff distance in any direction from any atom in the solute molecule.
-The correction scheme may not be applied when the solute and/or solvent molecule is comparable in size to
+**Caution**: The Lennard-Jones long-range correction scheme can be used only when the solvent distribution is homogeneous (radial distribution function is essentially unity) when the solvent molecule is separated beyond the Lennard-Jones cutoff distance in any direction from any atom in the solute molecule. The correction scheme may not be applied when the solute and/or solvent molecule is comparable in size to
 or larger than the cutoff radius, which is typically ~10 Angstrom, or when the solvent is inhomogeneous in nanoscale and, for example, is micelle or lipid membrane.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 26 Aug 2016 08:00:42 -0000

--- v3
+++ v4
@@ -1,7 +1,7 @@
 Long-range correction of the Lennard-Jones interaction
 ----

-The long-range correction of the Lennard-Jones interaction between the solute solvent can be computed in ERmod.
+The long-range correction of the Lennard-Jones interaction between the solute and solvent can be computed in ERmod.
 To enable this computation, it is enough to set ljlrc = 'yes' in parameters_fe as of ver 0.3.5
 and it is necessary to follow the procedures described at the end of this page when the version is 0.3.4 or earlier.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 26 Aug 2016 08:00:26 -0000

--- v2
+++ v3
@@ -2,22 +2,10 @@
 ----

 The long-range correction of the Lennard-Jones interaction between the solute solvent can be computed in ERmod.
-In the parent directory of the distributed ERmod package, there is a sub-directory extensions/LJLRC.
-The modifed slvfe.F90 program contained in that sub-directory can evaluate the long-range correction.
+To enable this computation, it is enough to set ljlrc = 'yes' in parameters_fe as of ver 0.3.5
+and it is necessary to follow the procedures described at the end of this page when the version is 0.3.4 or earlier.

-The slvfe.F90 program contained in the extensions/LJLRC directory has a key of ljlrc, which enables the Lennard-Jones long-range correction at ljlrc = 'yes'.
-To use the slvfe.F90 program contained in this directory, user simply does the followings in the parent directory of ERmod.
-
-~~~~
-::::sh
-mv slvfe.F90 slvfe_original.F90
-cp extensions/LJLRC/slvfe.F90 ./
-make
-make install
-~~~~
-
-Without stating ljlrc = 'yes' in parameters_fe, the modified slvfe works just as in the same way as the original slvfe.
-By setting ljlrc = 'yes' in parameters_fe, user is required to prepare a file contaning the average volume of the reference solvent, which is read, for example, as
+By setting ljlrc = 'yes' in parameters_fe, user is required to prepare a file contaning the average volume of the reference solvent, which is read, for example, as

 ~~~~
 ::::sh
@@ -35,8 +23,24 @@

 and is to type the average volume in Angstrom^3 directly on terminal.

-The difference between the original and modified slvfe.F90 is always updated in the diff_slvfe file in the extensions/LJLRC directory.
-
 **Caution**: The Lennard-Jones long-range correction scheme can be used only when the solvent distribution is homogeneous (radial distribution function is essentially unity) when the solvent molecule is separated beyond the Lennard-Jones cutoff distance in any direction from any atom in the solute molecule.
 The correction scheme may not be applied when the solute and/or solvent molecule is comparable in size to
 or larger than the cutoff radius, which is typically ~10 Angstrom, or when the solvent is inhomogeneous in nanoscale and, for example, is micelle or lipid membrane.
+
+
+When the version of ERmod is 0.3.4 or earlier, the following procedures are necessary.
+In the parent directory of the distributed ERmod package, there is a sub-directory extensions/LJLRC.
+The modifed slvfe.F90 program contained in that sub-directory can evaluate the long-range correction.
+The slvfe.F90 program contained in the extensions/LJLRC directory has a key of ljlrc, which enables the Lennard-Jones long-range correction at ljlrc = 'yes'.
+To use the slvfe.F90 program contained in this directory, user simply does the followings in the parent directory of ERmod.
+
+~~~~
+::::sh
+mv slvfe.F90 slvfe_original.F90
+cp extensions/LJLRC/slvfe.F90 ./
+make
+make install
+~~~~
+
+Without stating ljlrc = 'yes' in parameters_fe, the modified slvfe works just as in the same way as the original slvfe.
+The difference between the original and modified slvfe.F90 is written in the diff_slvfe file in the extensions/LJLRC directory.

LongRangeCorrectionLJ modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 18 Aug 2015 04:12:42 -0000

--- v1
+++ v2
@@ -16,7 +16,7 @@
 make install
 ~~~~

-Without stating ljlrc = 'yes' in parameters_fe, the modified slvfe works just as in the same way as the original slvfe.
+Without stating ljlrc = 'yes' in parameters_fe, the modified slvfe works just as in the same way as the original slvfe.
 By setting ljlrc = 'yes' in parameters_fe, user is required to prepare a file contaning the average volume of the reference solvent, which is read, for example, as

 ~~~~
@@ -26,7 +26,7 @@
 ~~~~

 The volumedata file simpy has the average volume of the reference solvent in Angstrom^3 unit; note that it not be given in nm^3.
-If the volumedata file is not present, user is asked
+If the volumedata file is not present, user is asked

 ~~~~
 ::::sh
@@ -35,8 +35,8 @@

 and is to type the average volume in Angstrom^3 directly on terminal.

-The difference between the original and modified slvfe.F90 is always updated in diff_slvfe in the extensions/LJLRC directory.
+The difference between the original and modified slvfe.F90 is always updated in the diff_slvfe file in the extensions/LJLRC directory.

-Caution: The Lennard-Jones long-range correction scheme can be used only when the solvent distribution is homogeneous (radial distribution function is essentially unity) when the solvent molecule is separated beyond the Lennard-Jones cutoff distance in any direction from any atom in the solute molecule.
+**Caution**: The Lennard-Jones long-range correction scheme can be used only when the solvent distribution is homogeneous (radial distribution function is essentially unity) when the solvent molecule is separated beyond the Lennard-Jones cutoff distance in any direction from any atom in the solute molecule.
 The correction scheme may not be applied when the solute and/or solvent molecule is comparable in size to
 or larger than the cutoff radius, which is typically ~10 Angstrom, or when the solvent is inhomogeneous in nanoscale and, for example, is micelle or lipid membrane.