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Commit fad8ceb0 authored by James Graham's avatar James Graham
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Update tutorial

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data/water.gro 0 → 100644
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WATER
400
1W W 1 0.084 3.595 3.359 0.0663 0.0148 0.2032
2W W 2 0.460 2.488 2.882 0.0999 -0.0648 -0.1661
3W W 3 3.165 2.218 0.652 -0.0881 -0.1237 -0.0896
4W W 4 3.295 3.303 2.679 -0.1486 -0.3229 0.1120
5W W 5 1.213 3.294 0.205 -0.1053 -0.1062 0.1014
6W W 6 1.296 1.446 1.188 0.0877 -0.0566 -0.1282
7W W 7 0.811 1.294 1.352 0.1967 0.2199 0.3289
8W W 8 1.802 2.109 0.786 -0.1596 -0.1576 -0.0010
9W W 9 1.477 3.201 3.141 -0.1225 0.0135 0.1267
10W W 10 0.126 0.762 3.104 0.0776 -0.1781 -0.1549
11W W 11 0.888 0.042 2.906 0.1622 -0.2895 -0.1539
12W W 12 2.582 0.430 1.793 0.0293 0.1399 0.1850
13W W 13 2.231 1.301 0.363 0.0119 0.0262 -0.0578
14W W 14 2.801 0.735 3.454 0.2122 -0.0713 -0.1525
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16W W 16 0.266 3.146 3.600 0.0972 -0.2452 0.1849
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26W W 26 1.085 1.718 3.011 0.1122 -0.2451 -0.0872
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29W W 29 2.093 2.634 2.844 -0.0502 -0.3423 -0.3093
30W W 30 1.313 1.274 2.069 0.2198 0.0937 0.0394
31W W 31 1.605 2.058 1.712 0.1814 0.5446 0.0734
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44W W 44 3.378 2.743 0.615 0.0989 0.0259 0.0111
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50W W 50 2.691 1.457 0.232 0.0327 -0.0493 0.0328
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52W W 52 1.705 0.931 1.571 0.0388 0.0230 -0.1394
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100W W 100 3.361 0.619 1.642 0.4842 -0.0207 0.5468
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108W W 108 2.446 2.029 3.486 0.3129 0.1316 0.1030
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281W W 281 1.593 1.682 2.117 0.1986 0.0823 0.0494
282W W 282 1.416 0.707 0.222 0.0137 -0.0803 0.2679
283W W 283 0.551 1.523 1.003 -0.4184 -0.0235 0.0295
284W W 284 0.322 3.375 2.440 0.0241 -0.3097 0.2289
285W W 285 3.117 1.601 0.548 0.1138 -0.3037 -0.0779
286W W 286 3.212 0.517 3.234 0.1463 -0.1522 0.1318
287W W 287 2.648 2.726 1.197 -0.4283 0.0105 -0.0491
288W W 288 0.246 1.650 3.374 0.1430 -0.2762 0.0584
289W W 289 3.212 0.114 0.670 0.2459 0.0850 -0.4919
290W W 290 2.732 2.589 0.681 -0.1231 0.0609 0.0336
291W W 291 1.634 1.647 0.766 -0.0282 -0.2216 -0.3378
292W W 292 2.821 0.451 0.289 0.0077 0.0950 0.0690
293W W 293 2.886 1.058 2.475 0.0722 0.1345 0.0404
294W W 294 0.595 1.651 1.682 -0.0289 -0.0903 0.0656
295W W 295 0.889 2.590 1.331 -0.3094 0.4324 0.0715
296W W 296 2.652 1.210 1.296 0.0531 0.2386 0.0526
297W W 297 1.675 0.589 1.992 -0.1765 -0.0275 0.0413
298W W 298 3.637 2.500 2.503 -0.0165 0.0744 0.6199
299W W 299 3.555 0.487 2.064 0.0899 0.0950 0.0222
300W W 300 0.094 3.317 1.440 0.0363 0.2081 0.1416
301W W 301 0.603 2.504 0.976 -0.2194 0.1315 -0.0227
302W W 302 0.518 0.121 3.529 -0.3937 0.3828 0.2951
303W W 303 1.637 2.974 3.631 -0.3231 0.1101 -0.0842
304W W 304 3.392 1.942 1.421 -0.2026 -0.3168 0.3117
305W W 305 2.746 2.119 0.301 -0.1762 -0.0749 -0.0256
306W W 306 2.041 3.640 2.513 0.1103 -0.0128 0.1930
307W W 307 2.898 2.362 3.550 -0.2284 0.0241 0.0767
308W W 308 1.713 0.072 0.830 -0.1401 0.1203 0.1327
309W W 309 2.426 0.941 1.689 -0.1412 -0.3995 -0.3513
310W W 310 0.112 2.528 2.021 -0.3497 0.0786 0.0228
311W W 311 1.365 0.490 0.662 0.2949 -0.2454 0.1967
312W W 312 1.169 1.974 3.511 -0.1810 -0.1150 0.3257
313W W 313 2.163 0.955 1.225 0.0111 -0.0602 -0.1369
314W W 314 2.368 2.365 2.347 0.0124 -0.0210 0.1854
315W W 315 0.522 2.970 2.782 -0.0240 0.0714 -0.0082
316W W 316 1.113 2.953 3.505 -0.0578 -0.0523 0.4016
317W W 317 0.964 0.750 0.519 -0.3118 -0.0358 -0.0294
318W W 318 2.481 0.892 0.844 0.0362 0.1892 -0.1742
319W W 319 2.439 3.000 3.081 -0.0106 -0.2847 -0.1368
320W W 320 1.124 1.592 1.680 0.1703 0.3131 0.0347
321W W 321 0.779 3.290 2.545 0.1385 -0.2117 -0.2508
322W W 322 3.524 3.407 0.146 -0.1664 0.1630 0.0233
323W W 323 0.387 2.079 3.142 0.0091 -0.0356 -0.0878
324W W 324 2.382 2.341 1.830 -0.1970 0.1099 0.1859
325W W 325 0.818 1.990 1.072 0.0571 0.0701 0.0504
326W W 326 1.189 2.997 2.467 0.2549 0.4989 0.2753
327W W 327 1.567 0.416 1.508 -0.0304 -0.0067 0.0017
328W W 328 0.178 2.400 0.438 -0.2204 -0.2920 -0.0494
329W W 329 1.697 1.351 0.308 0.0908 0.1461 0.0055
330W W 330 0.343 1.900 1.327 -0.0430 -0.3669 -0.1231
331W W 331 1.633 0.542 2.791 0.1245 0.0661 -0.2053
332W W 332 3.305 0.251 0.218 0.2771 -0.4176 -0.3080
333W W 333 3.398 1.997 3.317 0.1739 -0.2211 -0.3356
334W W 334 2.052 3.254 3.469 -0.0978 0.2432 -0.1600
335W W 335 3.610 2.348 2.991 -0.1393 0.0570 0.0705
336W W 336 3.018 3.146 3.602 0.0979 -0.0154 0.0675
337W W 337 0.757 3.602 2.080 -0.1619 -0.1484 0.3717
338W W 338 3.616 2.224 0.954 -0.0945 -0.1854 -0.1266
339W W 339 2.146 1.491 1.467 0.1428 -0.0216 0.1860
340W W 340 1.913 0.103 1.357 0.1154 0.2005 -0.0996
341W W 341 0.972 3.087 1.194 0.0561 -0.3476 0.0852
342W W 342 1.471 0.828 2.419 0.0362 -0.3901 0.0307
343W W 343 1.171 0.197 1.888 -0.1636 0.2570 -0.2182
344W W 344 0.234 3.019 0.436 -0.0294 -0.1106 -0.0601
345W W 345 2.050 2.383 1.154 0.0464 -0.1103 -0.1910
346W W 346 0.925 3.178 3.033 -0.3117 -0.0874 0.0261
347W W 347 0.402 2.001 0.729 -0.1724 -0.0188 0.0021
348W W 348 0.287 0.544 1.728 0.1331 -0.0856 0.1751
349W W 349 1.835 2.509 1.785 0.1764 -0.4253 0.0125
350W W 350 0.087 0.363 0.805 -0.0935 0.0513 0.0230
351W W 351 2.751 1.569 2.732 0.2966 0.0325 0.1324
352W W 352 2.628 0.955 0.304 -0.1393 -0.1196 -0.0924
353W W 353 3.145 2.627 1.952 -0.2149 0.0465 -0.0432
354W W 354 1.806 3.111 1.783 -0.0874 -0.0098 0.3045
355W W 355 1.218 3.215 0.694 0.0393 -0.1275 -0.1694
356W W 356 2.500 0.118 0.124 -0.1562 0.2264 0.0358
357W W 357 0.300 3.378 1.865 0.0193 -0.1698 0.1343
358W W 358 2.497 1.136 3.500 0.1513 0.0075 -0.0186
359W W 359 0.480 0.666 3.499 0.0831 -0.1698 0.1693
360W W 360 0.211 1.266 0.832 -0.0126 0.1583 -0.2169
361W W 361 0.902 1.255 0.557 -0.4227 -0.3078 -0.1509
362W W 362 2.665 1.582 3.374 0.0784 0.2991 -0.0845
363W W 363 1.008 1.863 2.083 -0.0415 0.1934 -0.3105
364W W 364 2.482 0.149 1.203 -0.1083 -0.0615 -0.2930
365W W 365 1.613 3.580 1.706 0.0204 -0.1087 -0.1716
366W W 366 2.827 3.042 2.643 0.1265 -0.0611 0.0173
367W W 367 2.411 3.191 1.754 0.1619 0.0130 -0.4041
368W W 368 2.430 2.171 1.348 -0.1017 0.0671 -0.2733
369W W 369 1.892 0.396 0.419 -0.1278 0.0346 -0.2232
370W W 370 3.573 0.024 1.141 -0.1586 0.1127 -0.2725
371W W 371 1.261 1.659 0.304 0.4082 -0.1876 0.1785
372W W 372 3.427 0.996 1.294 0.0834 -0.0538 0.4157
373W W 373 2.119 2.166 0.171 -0.3176 0.1516 0.0555
374W W 374 3.055 2.366 2.919 -0.0247 -0.2816 -0.3012
375W W 375 2.709 3.067 0.386 -0.1355 -0.1989 -0.2566
376W W 376 1.324 0.742 3.292 0.0955 -0.0797 0.5514
377W W 377 1.144 1.326 2.533 -0.0683 0.0474 -0.2325
378W W 378 3.236 2.821 2.810 -0.3311 -0.0287 -0.2906
379W W 379 2.336 0.771 3.187 0.1146 0.0371 -0.2916
380W W 380 0.180 1.242 2.964 -0.0441 -0.1830 -0.1295
381W W 381 1.940 1.719 2.690 -0.0144 0.0463 -0.1025
382W W 382 0.297 2.477 1.347 0.0757 -0.0251 -0.1316
383W W 383 0.444 1.774 2.237 -0.0694 -0.3087 0.0707
384W W 384 2.761 2.060 2.587 0.3107 0.2012 -0.0691
385W W 385 2.533 3.440 3.398 -0.0317 -0.1247 -0.1516
386W W 386 2.429 1.179 2.951 -0.1043 0.1520 -0.1340
387W W 387 2.706 3.233 1.356 0.0570 0.4550 -0.0556
388W W 388 1.708 2.953 2.679 0.3637 0.0704 0.0366
389W W 389 1.193 3.308 1.948 -0.0395 0.0042 -0.0031
390W W 390 2.998 2.479 2.367 0.3160 -0.0373 0.0552
391W W 391 2.048 2.551 3.504 -0.0849 -0.0297 0.1256
392W W 392 0.653 2.504 1.843 0.0882 -0.0692 -0.2940
393W W 393 2.999 2.263 1.488 0.1866 0.3055 0.3291
394W W 394 2.640 3.329 2.239 0.2390 0.1363 -0.0792
395W W 395 0.618 3.058 2.109 -0.0167 -0.0406 -0.0423
396W W 396 1.639 1.110 3.319 0.0300 -0.3053 0.0710
397W W 397 2.090 3.276 0.830 -0.0307 0.0044 0.1215
398W W 398 1.398 2.531 3.468 0.0631 -0.0196 -0.4235
399W W 399 1.524 2.769 0.845 -0.5337 0.0559 0.0075
400W W 400 0.745 1.509 0.104 0.1616 -0.0161 0.1005
3.64428 3.64428 3.64428
doc/source/pycgtool.warnings.rst deleted 100644 → 0
+ 0
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pycgtool.warnings module
========================
.. automodule:: pycgtool.warnings
:members:
:undoc-members:
:show-inheritance:
doc/source/tutorial.rst
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− 0
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......@@ -132,3 +132,17 @@ These samples were compared in the paper using an R script to generate a series
If the automatically generated parameters provide an accurate representation of the reference structure, the percentage error between the two samples will be small.
Validation of the more general molecular conformation may be performed by comparison of the radius of gyration of the reference and CG models.
This may be performed using the standard GROMACS too `gmx gyrate`::
gmx gyrate -f ref.xtc -s ref-for-rgyr.tpr -o ref-gyr.xvg
gmx gyrate -f md.xtc -s md.tpr -o cg-gyr.xvg
These commands will calculate the radius of gyration for each trajectory frame for both the reference and CG simulations.
The resulting `.xvg` files may be visualised using a graphing program such as `xmgrace` or compared in the same way as the bonded samples, using::
average_columns.py ref-gyr.xvg cg-gyr.xvg
As before, a small percentage difference in each of the columns suggests good replication of gross conformation.
In addition to these simple forms of validation, it is recommended that further validation, relevant to the class of molecule, is performed.
In the case of membane lipids, for instance, this may take the form of an assessment of membrane thickness and surface area per lipid.
doc/tutorial_files/Makefile
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all: pycgtool cgprepare em npt md
all: pycgtool cgprepare em npt md samples rgyr
pycgtool:
../../pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd
......@@ -20,9 +20,19 @@ md:
gmx grompp -f md.mdp -c npt.gro -p topol.top -o md.tpr
gmx mdrun -deffnm md -v
samples:
../../pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd --advanced
mv {36KB,ref}_length.dat
mv {36KB,ref}_angle.dat
../../pycgtool.py -g md.gro -x md.xtc -b atenolol.bnd
comparesamples:
./average_columns.py ref_length.dat 36KB_length.dat
./average_columns.py ref_angle.dat 36KB_angle.dat
rgyr:
gmx gyrate -f ref.xtc -s ref.tpr -o ref-gyr.xvg
gmx gyrate -f md.xtc -s md.tpr -o cg-gyr.xvg
echo 2 | gmx gyrate -f ref.xtc -s ref-for-rgyr.tpr -o ref-gyr.xvg
echo 2 | gmx gyrate -f md.xtc -s md.tpr -o cg-gyr.xvg
clean:
git clean -i
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