Recent changes to QuickStartGuide

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 07:12:54 -0000

--- v61
+++ v62
@@ -24,10 +24,12 @@

 From this point, there are three choices depending upon which MD program is being used 

+

 Running erdst: Obtaining the energy histogram with GROMACS
 ----

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:13:48 -0000

--- v60
+++ v61
@@ -290,5 +290,5 @@

 When the solvent is of a single species, the contribution from the "1st" solvent species is not separately shown and the self-energy of the solute is incorporated into the output values of the energy and free energy.

-It should be further noted, irrespective of the number of solvent species, that the self-energy is not incorporated into the aveuv.tt and flcuv.tt outputs of the ermod program described in [Outputs from ermod run](output).
-   
+It should be further noted, irrespective of the number of solvent species, that the self-energy is not incorporated into the aveuv.tt and flcuv.tt outputs of the erdst program described in [Outputs from erdst run](output).
+

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:13:18 -0000

--- v59
+++ v60
@@ -130,7 +130,7 @@
 This is the average sum of the interaction energy of the solute with all the solvent molecules.

 In the above example, the trajectory of the solution system is divided into 10 blocks, and the average solvation energy is obtained in each of the 10 blocks;
-the number of divisions of the solution MD is specified by the engdiv parameter within the parameters_er file in the soln directory as described in [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03), and its default value is 10.
+the number of divisions of the solution MD is specified by the engdiv parameter within the parameters_er file in the soln directory as described in [Parameter files for erdst](parameters-erdst), and its default value is 10.
 Each line then presents the cumulative average of the solvation energy and the 95% error (twice the standard error).
 For example, the 3rd line is the averaged solvation energy and the error, calculated from the first 3/10 of the trajectory of the solution system.
 If the error is too large, the simulation is not equilibrated well or the simulation time is insufficient.
@@ -205,7 +205,7 @@
 The trajectory is divided into a set of blocks both for soln and refs.
 The default value of the number of divisions is 10 for the solution system and is 5 for the reference solvent.
 The number of divisions can be modified with the engdiv parameter in the parameters_er file when the ermod program is run; engdiv can be changed independently for the soln and refs calculations through the respective parameters_er files.
-See [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03) for the description of the parameters which can be specified in parameters_er.
+See [Parameter files for erdst](parameters-erdst) for the description of the parameters which can be specified in parameters_er.

 Note that no block averaging is performed for the reference-solvent system.
 See [Assessing the convergence with respect to the reference-solvent calculation](refs-converge) for the procedure to examine the the convergence behavior of the solvation free energy with respect to the reference-solvent calculation.

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:11:29 -0000

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:11:14 -0000

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:10:45 -0000

--- v56
+++ v57
@@ -1,7 +1,7 @@
 Quick Start Guide
 ====

-This page describes how to install and use the ERMOD (Energy Representation MODule) program package.
+This page describes how to install and use the ERmod (Energy Representation MODule) program package.

 Obtaining Software
 ----

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:06:17 -0000

--- v55
+++ v56
@@ -24,22 +24,22 @@

 From this point, there are three choices depending upon which MD program is being used 

-Running ermod: Obtaining the energy histogram with NAMD
+Running erdst: Obtaining the energy histogram with NAMD
 ----

 Please see [Quick Start Guide/NAMD](QuickStartGuide-NAMD).

-Running ermod: Obtaining the energy histogram with GROMACS
+Running erdst: Obtaining the energy histogram with GROMACS
 ----

 Please see [Quick Start Guide/GROMACS](QuickStartGuide-GROMACS).

-Running ermod: Obtaining the energy histogram with AMBER
+Running erdst: Obtaining the energy histogram with AMBER
 ----

 Please see [Quick Start Guide/AMBER](QuickStartGuide-AMBER).

-Running ermod: Obtaining the energy histogram with LAMMPS
+Running erdst: Obtaining the energy histogram with LAMMPS
 ----

 Please see [Quick Start Guide/LAMMPS](QuickStartGuide-LAMMPS).

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 03:53:46 -0000

--- v54
+++ v55
@@ -50,8 +50,7 @@
 After obtaining the energy distribution functions in both the _solution_ and _reference-solvent_ systems,
 user moves to the top directory (the directory where he ran the gen_structure script) and runs the slvfe program. 

-~~~~
-::::sh
+~~~~sh
 (ERmod directory)/bin/slvfe
 ~~~~

QuickStartGuide modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 03:53:22 -0000

--- v53
+++ v54
@@ -1,4 +1,4 @@
-Quick Start Guide (for version 0.2.x and version 0.3.x)
+Quick Start Guide
 ====

 This page describes how to install and use the ERMOD (Energy Representation MODule) program package.

QuickStartGuide modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 15 Oct 2020 02:32:01 -0000

--- v52
+++ v53
@@ -168,6 +168,8 @@
 and the 10 values computed are used to determine the average and error.
 The 10 values corresponding to the blocks are listed in section (5).

+When numdiv = 1 in parameters_fe, the column for the 95% error is absent in the slvfe output.
+
 To construct the histogram, a set of meshes need to be introduced to the value of solute-solvent pair energy.
 It is thus necessary to examine whether the energy meshes employed are appropriate.
 The last column is prepared to examine the error due to introduction of energy meshes.
@@ -188,7 +190,7 @@

 ### (5) Value of Solvation Free Energy in Each Block

-In the above example, the trajectory of the _solution_ system is divided into 10 blocks, and the solvation free energy is obtained in each of the 10 blocks. In (5), all of the 10 values are listed. The list tends to be long because the listing is done at each value of group and further for each solvent species if the number of solvent species is more than 1.
+In the above example, the trajectory of the _solution_ system is divided into 10 blocks, and the solvation free energy is obtained in each of the 10 blocks. In (5), all of the 10 values are listed. The list tends to be long because the listing is done at each value of group and further for each solvent species if the number of solvent species is more than 1. When numdiv = 1 in parameters_fe, section (5) is absent in the slvfe output.

 ### (6) Solvation Free Energy: Cumulative Average