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non-cyclic 1d test

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This commit is contained in:
Daniel Bauer
2020-03-07 21:10:31 +01:00
parent d3a70520df
commit cd7bea063f
707 changed files with 3400420 additions and 226 deletions
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4
Cargo.lock generated
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@@ -1,3 +1,5 @@
# This file is automatically @generated by Cargo.
# It is not intended for manual editing.
[[package]]
name = "GSL"
version = "1.0.0"
@@ -293,7 +295,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
[[package]]
name = "wham"
version = "0.9.4"
version = "0.9.5"
dependencies = [
"GSL 1.0.0 (registry+https://github.com/rust-lang/crates.io-index)",
"clap 2.32.0 (registry+https://github.com/rust-lang/crates.io-index)",

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README.md
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@@ -88,12 +88,14 @@ 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: Hyaluronan-CD44 binding (See https://doi.org/10.1371/journal.pcbi.1005663)
- 1d_cyclic: Phi torsion angle of dialanine in vaccum
- 2d_cyclic: Phi and psi torsion angles of the same system
TODO
---
- better error estimation
- Autocorrelation
- Replica exchange

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Data is a subset of the umbrella simulation run in 10.1371/journal.pcbi.1005663
"Atomisticfingerprintofhyaluronan–CD44binding" by Vuirio et al.
Only a subset of the original files was used to reduce file size. Please
refer to the publication for more information and original files.
wham.out was produced with the following settings:
wham --min 0.7 --max 4.5
--bins 100
-T 310
-f metadata.dat
-o wham.out

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Example data: Dialanine torsion angle at 300K
wham.out was produced with the folling settings:
wham --max 3.14 --min -3.14 --cyclic\
--bins 100 \
-T 300 \
-f metadata.dat \
-o wham.out

25
example/1d_cyclic/metadata.dat Normal file
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@@ -0,0 +1,25 @@
COLVAR+0.0.xvg 0.0 100
COLVAR+0.25.xvg 0.25 100
COLVAR+0.5.xvg 0.5 100
COLVAR+0.75.xvg 0.75 100
COLVAR+1.0.xvg 1.0 100
COLVAR+1.25.xvg 1.25 100
COLVAR+1.5.xvg 1.5 100
COLVAR+1.75.xvg 1.75 100
COLVAR+2.0.xvg 2.0 100
COLVAR+2.25.xvg 2.25 100
COLVAR+2.5.xvg 2.5 100
COLVAR+2.75.xvg 2.75 100
COLVAR+3.0.xvg 3.0 100
COLVAR-0.25.xvg -0.25 100
COLVAR-0.5.xvg -0.5 100
COLVAR-0.75.xvg -0.75 100
COLVAR-1.0.xvg -1.0 100
COLVAR-1.25.xvg -1.25 100
COLVAR-1.5.xvg -1.5 100
COLVAR-1.75.xvg -1.75 100
COLVAR-2.0.xvg -2.0 100
COLVAR-2.25.xvg -2.25 100
COLVAR-2.5.xvg -2.5 100
COLVAR-2.75.xvg -2.75 100
COLVAR-3.0.xvg -3.0 100

101
example/1d_cyclic/wham.out Normal file
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#coord1 Free Energy +/- Probability +/-
-3.108600 7.118166 0.000000 0.003561 0.000000
-3.045800 5.331290 0.000000 0.007290 0.000000
-2.983000 3.879241 0.000000 0.013048 0.000000
-2.920200 2.968659 0.000000 0.018796 0.000000
-2.857400 1.942494 0.000000 0.028362 0.000000
-2.794600 1.418408 0.000000 0.034994 0.000000
-2.731800 1.169398 0.000000 0.038668 0.000000
-2.669000 0.843024 0.000000 0.044073 0.000000
-2.606200 0.636021 0.000000 0.047887 0.000000
-2.543400 0.720123 0.000000 0.046299 0.000000
-2.480600 1.066434 0.000000 0.040297 0.000000
-2.417800 1.509855 0.000000 0.033734 0.000000
-2.355000 2.015549 0.000000 0.027544 0.000000
-2.292200 2.226942 0.000000 0.025306 0.000000
-2.229400 2.573176 0.000000 0.022026 0.000000
-2.166600 2.591946 0.000000 0.021861 0.000000
-2.103800 2.476835 0.000000 0.022893 0.000000
-2.041000 2.513953 0.000000 0.022555 0.000000
-1.978200 2.470032 0.000000 0.022956 0.000000
-1.915400 2.227585 0.000000 0.025299 0.000000
-1.852600 2.105310 0.000000 0.026570 0.000000
-1.789800 1.778779 0.000000 0.030286 0.000000
-1.727000 1.447127 0.000000 0.034593 0.000000
-1.664200 0.906384 0.000000 0.042968 0.000000
-1.601400 0.304263 0.000000 0.054699 0.000000
-1.538600 0.247397 0.000000 0.055960 0.000000
-1.475800 0.000000 0.000000 0.061795 0.000000
-1.413000 0.536142 0.000000 0.049843 0.000000
-1.350200 1.428046 0.000000 0.034859 0.000000
-1.287400 2.398149 0.000000 0.023627 0.000000
-1.224600 3.784647 0.000000 0.013552 0.000000
-1.161800 5.696583 0.000000 0.006297 0.000000
-1.099000 7.656158 0.000000 0.002870 0.000000
-1.036200 9.955000 0.000000 0.001142 0.000000
-0.973400 12.357407 0.000000 0.000436 0.000000
-0.910600 14.954254 0.000000 0.000154 0.000000
-0.847800 17.745327 0.000000 0.000050 0.000000
-0.785000 20.559461 0.000000 0.000016 0.000000
-0.722200 22.783560 0.000000 0.000007 0.000000
-0.659400 25.175865 0.000000 0.000003 0.000000
-0.596600 26.419980 0.000000 0.000002 0.000000
-0.533800 27.885999 0.000000 0.000001 0.000000
-0.471000 29.029334 0.000000 0.000001 0.000000
-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

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example/2d/COLVAR+0.0-3.0.xvg → example/2d_cyclic/COLVAR+0.0-3.0.xvg
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example/2d/COLVAR+0.25+0.0.xvg → example/2d_cyclic/COLVAR+0.25+0.0.xvg
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example/2d/COLVAR+0.25+0.25.xvg → example/2d_cyclic/COLVAR+0.25+0.25.xvg
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example/2d/COLVAR+0.25+0.5.xvg → example/2d_cyclic/COLVAR+0.25+0.5.xvg
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example/2d/COLVAR+0.25+0.75.xvg → example/2d_cyclic/COLVAR+0.25+0.75.xvg
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example/2d/COLVAR+0.25+1.0.xvg → example/2d_cyclic/COLVAR+0.25+1.0.xvg
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example/2d/COLVAR+0.25+1.25.xvg → example/2d_cyclic/COLVAR+0.25+1.25.xvg
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example/2d/COLVAR+0.25+1.5.xvg → example/2d_cyclic/COLVAR+0.25+1.5.xvg
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