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alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
Creative Commons Attribution 4.0 International
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Sec 3 stat mech can tell us...
#82
ppxasjsm
closed
4 years ago
0
7.1.2 absolute free energies
#81
ppxasjsm
closed
4 years ago
0
7.2.1 and 7.2.2
#80
ppxasjsm
closed
4 years ago
2
7.2.3 alchemical pathway
#79
ppxasjsm
closed
4 years ago
8
7.2.4 sampling schemes
#78
ppxasjsm
closed
4 years ago
3
7.2.5 How long should I run my simulation for
#77
ppxasjsm
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4 years ago
0
7.2.6 multiple binding modes
#76
ppxasjsm
closed
4 years ago
0
Section 8.1-8.3
#75
ppxasjsm
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4 years ago
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Section 8.4 Uncertainty estimations
#74
ppxasjsm
closed
4 years ago
0
8.5 Are my simulations any good?
#73
ppxasjsm
closed
4 years ago
1
Section 8.6 Recommendations for analysis
#72
ppxasjsm
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4 years ago
0
Section 8.7 best practices for data representation
#71
ppxasjsm
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4 years ago
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Sec 9 Conclusions
#70
ppxasjsm
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4 years ago
2
Formatting and content of Sec 10, 11, 12 and 13
#69
ppxasjsm
closed
4 years ago
0
Figure 9 -- data and legibility
#68
ppxasjsm
closed
4 years ago
5
all figures and their captions
#67
ppxasjsm
closed
4 years ago
2
Edits to beginning of the document
#66
jchodera
closed
4 years ago
1
Review section on perturbation maps and cycle closure
#65
ppxasjsm
closed
4 years ago
0
Are we taking advantage of previous reviews?
#64
mrshirts
closed
4 years ago
8
formalize subsection vs subsection*?
#63
mrshirts
closed
4 years ago
3
Reference "basic simulation training" rather than giving a list here?
#62
davidlmobley
closed
4 years ago
2
Authorship proposal
#61
mrshirts
closed
4 years ago
3
How best to add new text?
#60
mrshirts
closed
4 years ago
3
[sec:8] Missing good analysis practice
#59
ppxasjsm
closed
4 years ago
4
[fig9_convergence]
#58
ppxasjsm
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4 years ago
0
[sec:8:estimators] references
#57
ppxasjsm
closed
4 years ago
3
[Sec:8] overall review required
#56
ppxasjsm
closed
4 years ago
3
[sec:The importance of the alchemical pathway]
#55
ppxasjsm
closed
4 years ago
2
[sec7:] what simulation protocol should I use
#54
ppxasjsm
closed
4 years ago
1
[Fig: perturbation network] Review
#53
ppxasjsm
closed
4 years ago
2
[Sec4:, sec:5, sec:6] tidy up
#52
ppxasjsm
closed
4 years ago
7
[Sec:4 Can I afford the calculation?]
#51
ppxasjsm
closed
4 years ago
1
[Sec:4 subsection] reproducibility:
#50
ppxasjsm
closed
4 years ago
3
[Sec:3] Theory Needs expansion
#49
ppxasjsm
closed
4 years ago
9
[Sec:1 and Sec:2] Review and check flow
#48
ppxasjsm
closed
4 years ago
1
Updates from Overleaf
#47
ppxasjsm
closed
4 years ago
0
Updates from Overleaf
#46
ppxasjsm
closed
4 years ago
0
compiling document fails with missing figures
#45
agrossfield
closed
4 years ago
2
Reference management?
#44
mrshirts
closed
4 years ago
4
Updates from Overleaf
#43
ppxasjsm
closed
4 years ago
0
Fig8/Fig9 sampling convergence and forward and backward
#42
ppxasjsm
closed
4 years ago
7
Updates from Overleaf
#41
ppxasjsm
closed
4 years ago
0
Softcoreplot
#40
mrshirts
closed
4 years ago
2
[Figure 1] What types of simulations can be run using alchemical simulations
#39
ppxasjsm
closed
4 years ago
13
[Figure 2] Illustrating lambda scheme figure [help]
#38
ppxasjsm
closed
4 years ago
9
[Figure X] Sampling schemes figure [help]
#37
ppxasjsm
closed
4 years ago
7
Add data and code used to generate Fig 7
#36
andrrizzi
closed
5 years ago
1
raw data for figure 7 -- convergence of DG from SAMPL
#35
ppxasjsm
closed
5 years ago
4
Updates from Overleaf
#34
ppxasjsm
closed
5 years ago
0
Section 7.+ Stopping conditions section for simulations
#33
ppxasjsm
closed
4 years ago
3
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