alchemistry alchemical-best-practices issues

alchemistry / alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal

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issues

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Finalise Overall Structure of V2

#132 fjclark opened 1 week ago
0
Some stuff to add to the next version.

#131 mrshirts opened 2 months ago
1
Discuss Newer Restraint Schemes for ABFE

#130 fjclark opened 4 months ago
0
Discuss Newer Restraint Schemes for ABFE

#129 fjclark opened 4 months ago
0
Add Perses / OpenFE (and potentially alchemiscale) to the list of tools mentioned

#128 apayne97 opened 1 year ago
1
Add discussion of Alchemical Transfer Method

#127 jchodera opened 2 years ago
0
Expand on nonequilibrium switching

#126 jchodera opened 2 years ago
1
Fig 3. Issue #124

#125 samarjeet opened 2 years ago
0
Dual Topology Figure

#124 samarjeet opened 2 years ago
4
add some description on WHAM?

#123 smutao opened 2 years ago
7
Possible typo with in-text reference to a figure

#122 jasmin-guven opened 3 years ago
0
A few typos and questions

#121 mkgilson opened 3 years ago
2
fix typo

#120 nosarthur closed 3 years ago
0
Figure 12 has inconsistent labels

#119 mrshirts opened 3 years ago
3
DOI included inconsistently in citations

#118 mrshirts closed 3 years ago
1
Some updates for publication of ASAP version

#117 mrshirts closed 3 years ago
0
adding version 1.0

#116 ppxasjsm closed 4 years ago
0
[revision] Fig2

#115 ppxasjsm closed 4 years ago
2
[review] conformation v configuration

#114 ppxasjsm closed 4 years ago
9
adding review responses merge from broken overleaf

#113 ppxasjsm closed 4 years ago
0
Add SI/Include example topology files in SI (later)

#112 davidlmobley opened 4 years ago
0
Update convergence OA-G6 and CB8-G3

#111 andrrizzi closed 4 years ago
0
Overleaf sync to github no longer works after migration

#110 davidlmobley closed 3 years ago
2
Fix fig 2 7

#109 JenkeScheen closed 4 years ago
0
[review] non-equilibrium methods

#108 ppxasjsm closed 4 years ago
10
[review] accuracy increase for longer simulations?

#107 ppxasjsm closed 4 years ago
6
[review] Morphing

#106 ppxasjsm closed 4 years ago
7
[review] Uncertainty estimates

#105 ppxasjsm closed 4 years ago
6
[review] Fonts in figures

#104 ppxasjsm closed 4 years ago
7
[review] Law of mass action and theory background

#103 ppxasjsm closed 4 years ago
9
[review] Nomenclature

#102 ppxasjsm closed 4 years ago
5
[review] Forcefield issues

#101 ppxasjsm closed 4 years ago
7
[review] use of alchemical methods in QM

#100 ppxasjsm closed 4 years ago
7
[review] Dealing with charges and changes in constraint length

#99 ppxasjsm closed 4 years ago
7
[review] Inclusion of Gromos

#98 ppxasjsm closed 4 years ago
4
[review] Figure 12

#97 ppxasjsm closed 4 years ago
5
[review] Section 7

#96 ppxasjsm closed 4 years ago
4
[review] Opinion on timesteps?

#95 ppxasjsm closed 4 years ago
14
[review] Section 4.1 issue

#94 ppxasjsm closed 4 years ago
3
[review] Fig 1 inconsistency

#93 ppxasjsm closed 4 years ago
3
Add JDC grant funding; fix NIH acknowledgement for DLM

#92 jchodera closed 4 years ago
0
Suggestions

#91 yunhuige closed 4 years ago
12
constraints, TI, gromacs

#90 vgapsys closed 4 years ago
2
Figure13 increasing font size

#89 hannahbrucemacdonald closed 4 years ago
0
Figure 13

#88 hannahbrucemacdonald closed 4 years ago
0
[WIP] JDC edits

#87 jchodera closed 4 years ago
4
complex binding stoichiometry and FEP

#86 ppxasjsm closed 4 years ago
0
Watch paragraphing

#85 davidlmobley closed 4 years ago
1
Section 2

#84 ppxasjsm closed 4 years ago
4
Introduction

#83 ppxasjsm closed 4 years ago
0