From 6630cad88c415afa0107df1553ef8fc7aa995d87 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Sun, 14 Apr 2019 11:55:10 -0700 Subject: [PATCH] add units of energy and time to the descriptions of the datasets - Gromacs - Amber - NAMD - see also https://github.com/alchemistry/alchemlyb/issues/75 --- src/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst | 2 ++ src/alchemtest/amber/bace_improper/descr.rst | 2 ++ src/alchemtest/amber/simplesolvated/descr.rst | 2 ++ src/alchemtest/gmx/benzene/descr.rst | 2 ++ src/alchemtest/gmx/expanded_ensemble/case_1/descr.rst | 2 ++ src/alchemtest/gmx/expanded_ensemble/case_2/descr.rst | 2 ++ src/alchemtest/gmx/expanded_ensemble/case_3/descr.rst | 2 ++ src/alchemtest/namd/tyr2ala/descr.rst | 2 ++ 8 files changed, 16 insertions(+) diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst b/src/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst index c441295..fff29bd 100644 --- a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst +++ b/src/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst @@ -19,6 +19,8 @@ Data Set Characteristics: core is used in vdw :Experimental Free Energy difference: -0.26 kcal/mol :Missing Values: None + :Energy unit: kcal/mol + :Time unit: ps :Date: Jan 2018 :Donor: Silicon Therapeutics :License: `CC0 `_ diff --git a/src/alchemtest/amber/bace_improper/descr.rst b/src/alchemtest/amber/bace_improper/descr.rst index 6eea491..a71e222 100644 --- a/src/alchemtest/amber/bace_improper/descr.rst +++ b/src/alchemtest/amber/bace_improper/descr.rst @@ -17,6 +17,8 @@ Data Set Characteristics: :Alchemical Pathway: vdw in ligand 1 --> vdw in ligand 2, softcore is used in vdw :Experimental Free Energy difference: N/A :Missing Values: None + :Energy unit: kcal/mol + :Time unit: ps :Date: Jan 2018 :Donor: Silicon Therapeutics :License: `CC0 `_ diff --git a/src/alchemtest/amber/simplesolvated/descr.rst b/src/alchemtest/amber/simplesolvated/descr.rst index 0c6a7f0..d025c1c 100644 --- a/src/alchemtest/amber/simplesolvated/descr.rst +++ b/src/alchemtest/amber/simplesolvated/descr.rst @@ -19,6 +19,8 @@ Data Set Characteristics: core is used in vdw :Experimental Free Energy difference: N/A :Missing Values: None + :Energy unit: kcal/mol + :Time unit: ps :Date: Oct 2017 :Donor: Silicon Therapeutics :License: `CC0 `_ diff --git a/src/alchemtest/gmx/benzene/descr.rst b/src/alchemtest/gmx/benzene/descr.rst index ab481a3..a3cbc9b 100644 --- a/src/alchemtest/gmx/benzene/descr.rst +++ b/src/alchemtest/gmx/benzene/descr.rst @@ -15,6 +15,8 @@ Data Set Characteristics: :Alchemical Pathway: vdw + coul --> vdw --> vacuum :Experimental Hydration Free Energy: -0.90 +- 0.2 kcal/mol :Missing Values: None + :Energy unit: kJ/mol + :Time unit: ps :Creator: \I. Kenney :Donor: Ian Kenney (ian.kenney@asu.edu) :Date: March 2017 diff --git a/src/alchemtest/gmx/expanded_ensemble/case_1/descr.rst b/src/alchemtest/gmx/expanded_ensemble/case_1/descr.rst index 095a5b1..4fd338a 100644 --- a/src/alchemtest/gmx/expanded_ensemble/case_1/descr.rst +++ b/src/alchemtest/gmx/expanded_ensemble/case_1/descr.rst @@ -14,6 +14,8 @@ Data Set Characteristics: :Temperature: 300 K :Alchemical Pathway: vdw + coul --> vdw --> vacuum :Missing Values: None + :Energy unit: kJ/mol + :Time unit: ps :Creator: \T. Jensen :Donor: Travis Jensen (travis.jensen@colorado.edu) :Date: November 2017 diff --git a/src/alchemtest/gmx/expanded_ensemble/case_2/descr.rst b/src/alchemtest/gmx/expanded_ensemble/case_2/descr.rst index 6899011..829eaa4 100644 --- a/src/alchemtest/gmx/expanded_ensemble/case_2/descr.rst +++ b/src/alchemtest/gmx/expanded_ensemble/case_2/descr.rst @@ -14,6 +14,8 @@ Data Set Characteristics: :Temperature: 300 K :Alchemical Pathway: vdw + coul --> vdw --> vacuum :Missing Values: None + :Energy unit: kJ/mol + :Time unit: ps :Creator: \T. Jensen :Donor: Travis Jensen (travis.jensen@colorado.edu) :Date: November 2017 diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/descr.rst b/src/alchemtest/gmx/expanded_ensemble/case_3/descr.rst index 29539a4..04b3a97 100644 --- a/src/alchemtest/gmx/expanded_ensemble/case_3/descr.rst +++ b/src/alchemtest/gmx/expanded_ensemble/case_3/descr.rst @@ -14,6 +14,8 @@ Data Set Characteristics: :Temperature: 300 K :Alchemical Pathway: vdw + coul --> vdw --> vacuum :Missing Values: None + :Energy unit: kJ/mol + :Time unit: ps :Creator: \T. Jensen :Donor: Travis Jensen (travis.jensen@colorado.edu) :Date: November 2017 diff --git a/src/alchemtest/namd/tyr2ala/descr.rst b/src/alchemtest/namd/tyr2ala/descr.rst index 960744f..959a585 100644 --- a/src/alchemtest/namd/tyr2ala/descr.rst +++ b/src/alchemtest/namd/tyr2ala/descr.rst @@ -19,6 +19,8 @@ Data Set Characteristics: atoms are scaled with their environment. :Experimental Free Energy difference: N/A :Missing Values: None + :Energy unit: kcal/mol + :Time unit: step :Date: Oct 2017 :Donor: JC Gumbart :License: `CC0 `_