Recent changes to Home

Home modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 21 Jan 2025 08:10:14 -0000

--- v74
+++ v75
@@ -37,6 +37,7 @@
 * [Free energy calculation of protein solvation with explicit solvent](ProteinSolvation)
 * [Ligand-binding into protein at fixed ligand-protein configuration](FixedLigandBind)
 * [Generating EcdInfo semi-automatically](tips-ecdinfo)
+*  [Reducing the computation time for slvfe](OpenMP_slvfe)
 * [How to use mol_dissect](tools-mol_dissect) (ver 0.3)

 # FAQ

Home modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 21 Jan 2025 08:08:31 -0000

--- v73
+++ v74
@@ -28,7 +28,6 @@
 * [Sampling interval of MD](sample-skpcnf)
 * [Debugging practice for the reference-solvent calculation](debug-practice)
 * [To read a trajectory format which is not supported in VMD plugins](SpecialTrajFormat)
-*  [Reducing the computation time for slvfe](OpenMP_slvfe)

 # Advanced Guides

Home modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 09 Dec 2024 07:18:36 -0000

--- v72
+++ v73
@@ -13,8 +13,6 @@
 # [Outputs from erdst run](output)

 # [Build Guide](build-Guide)
-
-Want to run program on SPARC? Or Itanium? Then this is a guide for you!

 * [General build guide](build-Guide)
 * [Build guides for supercomputers](build-Supercom)

Home modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sun, 08 Dec 2024 06:41:01 -0000

--- v71
+++ v72
@@ -2,7 +2,7 @@

 # [Quick Start Guide](QuickStartGuide)

-* New to ERMOD? Please read [this guide](QuickStartGuide) first!
+* New to ERmod? Please read [this guide](QuickStartGuide) first!

 # Parameters

Home modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 19 Sep 2024 02:20:00 -0000

--- v70
+++ v71
@@ -30,6 +30,7 @@
 * [Sampling interval of MD](sample-skpcnf)
 * [Debugging practice for the reference-solvent calculation](debug-practice)
 * [To read a trajectory format which is not supported in VMD plugins](SpecialTrajFormat)
+*  [Reducing the computation time for slvfe](OpenMP_slvfe)

 # Advanced Guides

Home modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:26:14 -0000

--- v69
+++ v70
@@ -10,7 +10,7 @@
 * [Parameter files for slvfe](parameters-slvfe)
 * [Parameter files for ermod (ver 0.2)](parameters-ermod02)

-# [Outputs from ermod run](output)
+# [Outputs from erdst run](output)

 # [Build Guide](build-Guide)

Home modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 18 Apr 2024 08:02:28 -0000

--- v68
+++ v69
@@ -57,9 +57,9 @@

 # Migration Guides

+* [Migration from 0.3 to 1.0](MigrationGuide0310)
+* [Migration from 0.2 to 0.3](MigrationGuide0203)
 * [Migration from 0.1 to 0.2](MigrationGuide0102)
-* [Migration from 0.2 to 0.3](MigrationGuide0203)
-* [Migration from 0.3 to 1.0](MigrationGuide0310)

 # [Benchmarks](benchmark)

Home modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 09:15:27 -0000

--- v67
+++ v68
@@ -1,4 +1,4 @@
-ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program calculates the solvation free energy in arbitrary solvent, including inhomogeneous system, without requiring tuning parameters for specific solvent species. It can run in cooperation with state-of-art molecular simulation softwares, such as NAMD, GROMACS and/or AMBER.
+ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program calculates the solvation free energy in arbitrary solvent, including inhomogeneous system, without requiring tuning parameters for specific solvent species. It can run in cooperation with state-of-art molecular simulation softwares, such as LAMMPS, GROMACS and/or AMBER.

 # [Quick Start Guide](QuickStartGuide)

Home modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:15:08 -0000

--- v66
+++ v67
@@ -44,10 +44,10 @@
 # FAQ

 * [Frequently asked questions at the installation](FAQ_install)
-* [Frequently asked questions at running the ermod program](FAQ_running)
+* [Frequently asked questions at running the erdst program](FAQ_running)
 * [Handling output files](HandleOutputFiles)
 * [Error in gen_structure: IndexError: list index out of range](IndexOut_of_Range)
-* [Error in ermod: The minimum of the energy coordinate is too large](TooLargeMinimum)
+* [Error in erdst: The minimum of the energy coordinate is too large](TooLargeMinimum)
 * [Error in slvfe: Incorrect normalization at _(integer value)_](IncorrectNormalization)
 * [Warning in slvfe: mesh error is _(real value1)_ kcal/mol and is larger than the recommended value of _(real value2)_ kcal/mol](MeshErrorLargerThanRecommend)

@@ -59,6 +59,7 @@

 * [Migration from 0.1 to 0.2](MigrationGuide0102)
 * [Migration from 0.2 to 0.3](MigrationGuide0203)
+* [Migration from 0.3 to 1.0](MigrationGuide0310)

 # [Benchmarks](benchmark)

Home modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 04:05:38 -0000

--- v65
+++ v66
@@ -6,7 +6,7 @@

 # Parameters

-* [Parameter files for ermod](parameters-erdst)
+* [Parameter files for erdst](parameters-erdst)
 * [Parameter files for slvfe](parameters-slvfe)
 * [Parameter files for ermod (ver 0.2)](parameters-ermod02)