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3
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vendored
3
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[package]
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authors = ["D. Bauer <bauer@bio.tu-darmstadt.de>"]
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authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
|
||||
description = "An implementation of the weighted histogram analysis method"
|
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license = "GPL-3.0"
|
||||
repository = "https://github.com/danijoo/WHAM"
|
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@@ -11,6 +11,10 @@ clap = {version="2.32.0", features=['yaml']}
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[profile.release]
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opt-level = 2
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||||
|
||||
19
README.md
19
README.md
@@ -1,4 +1,6 @@
|
||||
[](https://travis-ci.com/danijoo/WHAM) [](https://www.crates.io/crates/wham)
|
||||
[](https://travis-ci.com/danijoo/WHAM) [](https://www.crates.io/crates/wham) [](https://doi.org/10.5281/zenodo.1488597)
|
||||
|
||||
|
||||
|
||||
Weighted Histogram Analysis Method (WHAM)
|
||||
===
|
||||
@@ -10,6 +12,7 @@ from umbrella sampling simulations. For more details on the method, I suggest *R
|
||||
Features
|
||||
---
|
||||
- Fast, especially for small systems
|
||||
- Multithreaded
|
||||
- Multidimensional
|
||||
- Error analysis
|
||||
- Unit tested
|
||||
@@ -78,27 +81,29 @@ one can estimate the error as standard deviation between the N bootstrapping run
|
||||
Autocorrelation Estimates, JCTC, 6(12), 3713-3720*.
|
||||
|
||||
To perform bayesian bootstrapping in WHAM, use the ```-bt <RUNS>``` flag to perform <RUNS> individual bootstrapping
|
||||
runs. The error estimates of bin probabilities and free energy will be given as separate column (+/-) in the output file.
|
||||
If no error analysis is performed, these columns are set to 0.0.
|
||||
runs. The error estimates of bin probabilities and free energy will be given as standard error (SE) in a
|
||||
separate column (+/-) in the output file. If no error analysis is performed, these columns are set to 0.0.
|
||||
|
||||
Examples
|
||||
---
|
||||
The example folder contains input and output files for two simple test systems:
|
||||
|
||||
- 1d: Phi torsion angle of dialanine in vaccum
|
||||
- 2d: Phi and psi torsion angles of the same system
|
||||
- 1d_cyclic: Phi torsion angle of dialanine in vaccum
|
||||
- 2d_cyclic: Phi and psi torsion angles of the same system
|
||||
|
||||
|
||||
TODO
|
||||
---
|
||||
- Multithreading (?)
|
||||
- better error estimation
|
||||
- Autocorrelation
|
||||
- Replica exchange
|
||||
|
||||
License
|
||||
License & Citing
|
||||
---
|
||||
WHAM is licensed under the GPL-3.0 license. Please read the LICENSE file in this
|
||||
repository for more information.
|
||||
|
||||
There's no publication for this WHAM implementation. However, there is a citeabe DOI. If you use this software for your work, please consider citing it: *Bauer, D, WHAM - An efficient weighted histogram analysis implementation written in Rust, Zenodo. https://doi.org/10.5281/zenodo.1488597*
|
||||
|
||||
Parts of this work, especially some perfomance optimizations and the I/O format, are inspired by the
|
||||
implementation of A. Grossfield (*Grossfield, A, WHAM: the weighted histogram analysis method, http://membrane.urmc.rochester.edu/content/wham*).
|
||||
|
||||
@@ -1,101 +0,0 @@
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||||
#coord1 Free Energy +/- Probability +/-
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|
||||
-0.408200 30.366556 0.000000 0.000000 0.000000
|
||||
-0.345400 31.615252 0.000000 0.000000 0.000000
|
||||
-0.282600 32.781716 0.000000 0.000000 0.000000
|
||||
-0.219800 33.731378 0.000000 0.000000 0.000000
|
||||
-0.157000 34.476014 0.000000 0.000000 0.000000
|
||||
-0.094200 35.387300 0.000000 0.000000 0.000000
|
||||
-0.031400 35.579756 0.000000 0.000000 0.000000
|
||||
0.031400 35.520194 0.000000 0.000000 0.000000
|
||||
0.094200 35.344763 0.000000 0.000000 0.000000
|
||||
0.157000 34.886460 0.000000 0.000000 0.000000
|
||||
0.219800 33.633998 0.000000 0.000000 0.000000
|
||||
0.282600 32.686511 0.000000 0.000000 0.000000
|
||||
0.345400 31.211777 0.000000 0.000000 0.000000
|
||||
0.408200 29.680451 0.000000 0.000000 0.000000
|
||||
0.471000 28.032242 0.000000 0.000001 0.000000
|
||||
0.533800 26.439599 0.000000 0.000002 0.000000
|
||||
0.596600 24.432467 0.000000 0.000003 0.000000
|
||||
0.659400 22.309893 0.000000 0.000008 0.000000
|
||||
0.722200 20.186040 0.000000 0.000019 0.000000
|
||||
0.785000 18.295046 0.000000 0.000040 0.000000
|
||||
0.847800 16.221232 0.000000 0.000093 0.000000
|
||||
0.910600 14.251911 0.000000 0.000204 0.000000
|
||||
0.973400 12.562353 0.000000 0.000402 0.000000
|
||||
1.036200 11.184029 0.000000 0.000698 0.000000
|
||||
1.099000 10.040677 0.000000 0.001103 0.000000
|
||||
1.161800 9.369064 0.000000 0.001444 0.000000
|
||||
1.224600 9.095392 0.000000 0.001612 0.000000
|
||||
1.287400 9.256035 0.000000 0.001511 0.000000
|
||||
1.350200 9.814068 0.000000 0.001208 0.000000
|
||||
1.413000 10.945207 0.000000 0.000768 0.000000
|
||||
1.475800 12.518898 0.000000 0.000409 0.000000
|
||||
1.538600 14.409744 0.000000 0.000191 0.000000
|
||||
1.601400 16.451965 0.000000 0.000084 0.000000
|
||||
1.664200 18.589166 0.000000 0.000036 0.000000
|
||||
1.727000 20.669504 0.000000 0.000016 0.000000
|
||||
1.789800 22.804791 0.000000 0.000007 0.000000
|
||||
1.852600 24.531690 0.000000 0.000003 0.000000
|
||||
1.915400 26.182612 0.000000 0.000002 0.000000
|
||||
1.978200 27.279439 0.000000 0.000001 0.000000
|
||||
2.041000 28.571380 0.000000 0.000001 0.000000
|
||||
2.103800 29.328969 0.000000 0.000000 0.000000
|
||||
2.166600 29.897739 0.000000 0.000000 0.000000
|
||||
2.229400 30.320908 0.000000 0.000000 0.000000
|
||||
2.292200 30.065391 0.000000 0.000000 0.000000
|
||||
2.355000 29.809137 0.000000 0.000000 0.000000
|
||||
2.417800 29.340601 0.000000 0.000000 0.000000
|
||||
2.480600 28.473346 0.000000 0.000001 0.000000
|
||||
2.543400 27.679353 0.000000 0.000001 0.000000
|
||||
2.606200 26.453160 0.000000 0.000002 0.000000
|
||||
2.669000 24.424649 0.000000 0.000003 0.000000
|
||||
2.731800 22.285933 0.000000 0.000008 0.000000
|
||||
2.794600 19.958407 0.000000 0.000021 0.000000
|
||||
2.857400 17.606291 0.000000 0.000053 0.000000
|
||||
2.920200 15.420138 0.000000 0.000128 0.000000
|
||||
2.983000 13.069599 0.000000 0.000328 0.000000
|
||||
3.045800 11.036085 0.000000 0.000740 0.000000
|
||||
3.108600 9.015657 0.000000 0.001664 0.000000
|
||||
9
example/1d_cyclic/README.txt
Normal file
9
example/1d_cyclic/README.txt
Normal file
@@ -0,0 +1,9 @@
|
||||
Example data: Dialanine torsion angle at 300K
|
||||
wham.out was produced with the folling settings:
|
||||
|
||||
wham --max pi --min -pi --cyclic\
|
||||
--bins 100 \
|
||||
-T 300 \
|
||||
-f metadata.dat \
|
||||
-o wham.out \
|
||||
--bt 100 --seed 1234
|
||||
101
example/1d_cyclic/wham.out
Normal file
101
example/1d_cyclic/wham.out
Normal file
@@ -0,0 +1,101 @@
|
||||
#coord1 Free Energy +/- Probability +/-
|
||||
-3.110177 7.158102 0.069244 0.003494 0.000067
|
||||
-3.047345 5.365727 0.068503 0.007168 0.000135
|
||||
-2.984513 3.873190 0.065883 0.013039 0.000226
|
||||
-2.921681 2.953162 0.066856 0.018855 0.000334
|
||||
-2.858849 1.949554 0.066705 0.028195 0.000501
|
||||
-2.796017 1.391747 0.064012 0.035261 0.000576
|
||||
-2.733186 1.128270 0.061522 0.039189 0.000598
|
||||
-2.670354 0.839970 0.060810 0.043991 0.000653
|
||||
-2.607522 0.624769 0.061888 0.047955 0.000733
|
||||
-2.544690 0.663757 0.062566 0.047211 0.000736
|
||||
-2.481858 1.051932 0.061093 0.040407 0.000616
|
||||
-2.419026 1.463048 0.062547 0.034267 0.000543
|
||||
-2.356194 1.990616 0.057022 0.027734 0.000373
|
||||
-2.293363 2.190692 0.044029 0.025597 0.000202
|
||||
-2.230531 2.553036 0.041867 0.022136 0.000157
|
||||
-2.167699 2.572522 0.044817 0.021964 0.000184
|
||||
-2.104867 2.472360 0.038778 0.022863 0.000155
|
||||
-2.042035 2.517562 0.030296 0.022453 0.000150
|
||||
-1.979203 2.469778 0.025852 0.022887 0.000167
|
||||
-1.916372 2.223125 0.030799 0.025266 0.000411
|
||||
-1.853540 2.080157 0.024928 0.026756 0.000365
|
||||
-1.790708 1.793841 0.027529 0.030011 0.000475
|
||||
-1.727876 1.458784 0.026130 0.034326 0.000462
|
||||
-1.665044 0.914441 0.024774 0.042697 0.000576
|
||||
-1.602212 0.303813 0.020400 0.054540 0.000701
|
||||
-1.539380 0.268335 0.020423 0.055321 0.000733
|
||||
-1.476549 0.000000 0.020271 0.061604 0.000835
|
||||
-1.413717 0.537061 0.023895 0.049671 0.000735
|
||||
-1.350885 1.439940 0.023678 0.034586 0.000528
|
||||
-1.288053 2.391838 0.025951 0.023614 0.000386
|
||||
-1.225221 3.779470 0.026215 0.013538 0.000224
|
||||
-1.162389 5.685555 0.028543 0.006305 0.000109
|
||||
-1.099557 7.661896 0.030579 0.002855 0.000051
|
||||
-1.036726 9.946594 0.039243 0.001142 0.000022
|
||||
-0.973894 12.359408 0.054067 0.000434 0.000009
|
||||
-0.911062 14.954655 0.066597 0.000153 0.000004
|
||||
-0.848230 17.742242 0.073582 0.000050 0.000002
|
||||
-0.785398 20.555785 0.074644 0.000016 0.000001
|
||||
-0.722566 22.811160 0.078503 0.000007 0.000000
|
||||
-0.659734 25.178094 0.088961 0.000003 0.000000
|
||||
-0.596903 26.442288 0.093509 0.000002 0.000000
|
||||
-0.534071 27.897565 0.091353 0.000001 0.000000
|
||||
-0.471239 29.062473 0.086244 0.000001 0.000000
|
||||
-0.408407 30.384521 0.084285 0.000000 0.000000
|
||||
-0.345575 31.638454 0.084871 0.000000 0.000000
|
||||
-0.282743 32.817727 0.092750 0.000000 0.000000
|
||||
-0.219911 33.770369 0.094479 0.000000 0.000000
|
||||
-0.157080 34.505503 0.095774 0.000000 0.000000
|
||||
-0.094248 35.431659 0.107598 0.000000 0.000000
|
||||
-0.031416 35.615810 0.108959 0.000000 0.000000
|
||||
0.031416 35.561946 0.107382 0.000000 0.000000
|
||||
0.094248 35.382089 0.096643 0.000000 0.000000
|
||||
0.157080 34.934827 0.107624 0.000000 0.000000
|
||||
0.219911 33.673460 0.100231 0.000000 0.000000
|
||||
0.282743 32.731563 0.096604 0.000000 0.000000
|
||||
0.345575 31.261855 0.099036 0.000000 0.000000
|
||||
0.408407 29.717377 0.107915 0.000000 0.000000
|
||||
0.471239 28.076620 0.104513 0.000001 0.000000
|
||||
0.534071 26.481097 0.103164 0.000002 0.000000
|
||||
0.596903 24.487358 0.103039 0.000003 0.000000
|
||||
0.659734 22.344251 0.100666 0.000008 0.000000
|
||||
0.722566 20.241543 0.102150 0.000018 0.000001
|
||||
0.785398 18.341869 0.101957 0.000039 0.000002
|
||||
0.848230 16.261582 0.105391 0.000091 0.000005
|
||||
0.911062 14.301801 0.107389 0.000199 0.000010
|
||||
0.973894 12.603788 0.105487 0.000394 0.000020
|
||||
1.036726 11.249601 0.106308 0.000678 0.000035
|
||||
1.099557 10.087886 0.106741 0.001079 0.000055
|
||||
1.162389 9.443303 0.106957 0.001398 0.000071
|
||||
1.225221 9.152799 0.105940 0.001570 0.000079
|
||||
1.288053 9.331937 0.105860 0.001462 0.000074
|
||||
1.350885 9.905546 0.105389 0.001161 0.000058
|
||||
1.413717 11.042050 0.105466 0.000736 0.000037
|
||||
1.476549 12.598167 0.105119 0.000395 0.000020
|
||||
1.539380 14.520167 0.104367 0.000183 0.000009
|
||||
1.602212 16.569783 0.104184 0.000080 0.000004
|
||||
1.665044 18.687390 0.104276 0.000034 0.000002
|
||||
1.727876 20.775408 0.104944 0.000015 0.000001
|
||||
1.790708 22.905200 0.101547 0.000006 0.000000
|
||||
1.853540 24.643852 0.103914 0.000003 0.000000
|
||||
1.916372 26.301740 0.101973 0.000002 0.000000
|
||||
1.979203 27.372071 0.101762 0.000001 0.000000
|
||||
2.042035 28.697726 0.105177 0.000001 0.000000
|
||||
2.104867 29.417901 0.100003 0.000000 0.000000
|
||||
2.167699 30.008351 0.100038 0.000000 0.000000
|
||||
2.230531 30.406016 0.096233 0.000000 0.000000
|
||||
2.293363 30.171275 0.096428 0.000000 0.000000
|
||||
2.356194 29.884646 0.108339 0.000000 0.000000
|
||||
2.419026 29.428153 0.106679 0.000000 0.000000
|
||||
2.481858 28.546982 0.123259 0.000001 0.000000
|
||||
2.544690 27.757520 0.108526 0.000001 0.000000
|
||||
2.607522 26.505787 0.111134 0.000001 0.000000
|
||||
2.670354 24.491866 0.095963 0.000003 0.000000
|
||||
2.733186 22.320664 0.096576 0.000008 0.000000
|
||||
2.796017 20.052723 0.098813 0.000020 0.000001
|
||||
2.858849 17.655650 0.097052 0.000052 0.000002
|
||||
2.921681 15.471590 0.100497 0.000125 0.000005
|
||||
2.984513 13.138167 0.092102 0.000318 0.000011
|
||||
3.047345 11.092386 0.081862 0.000722 0.000020
|
||||
3.110177 9.065722 0.072111 0.001626 0.000034
|
||||
10001
example/2d/wham.out
10001
example/2d/wham.out
File diff suppressed because it is too large
Load Diff
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user