Principal Components as Collective Variables for Metadynamics - Help?
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billy.willi...@gmail.com
Dec 19, 2017, 1:45:05 AM12/19/17
to PLUMED users
Hi All,
I am looking for a step-by-step guide on how to perform metadynamics with Plumed, using principal components as the collective variables.
I have looked through the mailing list here and found this user sharing a script
Here the user uses this script as input:
Separately, I have performed PCA with the following command:
With plumed-pca.dat containing this input:
pca-comp.pdb is attached here. My understanding is that the first two principal components based on the variation in atoms 1-89 from my trajectory are included in this file. I read that from an online tutorial here
If I am understanding correctly, how would I used these principal components as CVs for metadynamics? I cannot find the syntax or an explanation for how online, and any help would be appreciated.
Cheers,
Billy
I am looking for a step-by-step guide on how to perform metadynamics with Plumed, using principal components as the collective variables.
I have looked through the mailing list here and found this user sharing a script
Here the user uses this script as input:
PRINT W_STRIDE 1000
HILLS W_STRIDE 1000 HEIGHT 0.4
PCA FRAME ref.dat EIGENVEC evec1.dat SIGMA 0.1
ENDMETA
Can somebody please refer me to a reference describing the exact steps used to generate ref.dat and evec1.dat, and what these files contain?HILLS W_STRIDE 1000 HEIGHT 0.4
PCA FRAME ref.dat EIGENVEC evec1.dat SIGMA 0.1
ENDMETA
Separately, I have performed PCA with the following command:
plumed driver --plumed plumed-pca.dat --mf_trr md-thin.trr --trajectory-stride 500
With plumed-pca.dat containing this input:
PCA METRIC=OPTIMAL ATOMS=1-89 STRIDE=1 NLOW_DIM=2 OFILE=pca-comp.pdb
pca-comp.pdb is attached here. My understanding is that the first two principal components based on the variation in atoms 1-89 from my trajectory are included in this file. I read that from an online tutorial here
If I am understanding correctly, how would I used these principal components as CVs for metadynamics? I cannot find the syntax or an explanation for how online, and any help would be appreciated.
Cheers,
Billy
Gareth Tribello
Dec 19, 2017, 1:09:38 PM12/19/17
to plumed...@googlegroups.com
Hello
Try looking at the manual page for PCAVARS.
You should be able to use the output from your PCA calculation as the reference file input for the PCAVARS command.
Please don’t expect rapid answers to follow up questions. I am on holiday for the next two weeks.
Merry Christamas
Gareth
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<pca-comp.pdb>
Billy Noonan
Jan 9, 2018, 10:51:36 PM1/9/18
to PLUMED users
Thank you for your quick response, Gareth!
This input seems to be working! I thought I would post it here in case anyone new wanted to look for it in future.
Cheers,
Billy
This input seems to be working! I thought I would post it here in case anyone new wanted to look for it in future.
PCAVARS REFERENCE=pca-comp.pdb TYPE=OPTIMAL LABEL=pca2
METAD ...
LABEL=metad
ARG=pca2.eig-1,pca2.eig-2
PACE=1000
HEIGHT=0.4
SIGMA=0.1,0.1
BIASFACTOR=15
GRID_MIN=-8,-8
GRID_MAX=8,8
GRID_SPACING=0.05,0.05
FILE=HILLS_PCA
TEMP=300.0
... METAD
# monitor the two variables and the metadynamics bias potential
PRINT ARG=pca2.eig-1,pca2.eig-2,pca2.residual,metad.bias FILE=COLVAR-PCA
Hope you had a merry Christmas and a Happy New Year too.METAD ...
LABEL=metad
ARG=pca2.eig-1,pca2.eig-2
PACE=1000
HEIGHT=0.4
SIGMA=0.1,0.1
BIASFACTOR=15
GRID_MIN=-8,-8
GRID_MAX=8,8
GRID_SPACING=0.05,0.05
FILE=HILLS_PCA
TEMP=300.0
... METAD
# monitor the two variables and the metadynamics bias potential
PRINT ARG=pca2.eig-1,pca2.eig-2,pca2.residual,metad.bias FILE=COLVAR-PCA
Cheers,
Billy
qingh...@gmail.com
Jan 10, 2018, 6:03:04 AM1/10/18
to PLUMED users
Hello Billy,
Thanks for sharing your input file, could you please also share your input pdb file (pca-comp.pdb)? That would be better for understanding! Thanks!
All the best,
Qinghua
Thanks for sharing your input file, could you please also share your input pdb file (pca-comp.pdb)? That would be better for understanding! Thanks!
All the best,
Qinghua
Message has been deleted
Billy Noonan
Jan 15, 2018, 12:11:20 AM1/15/18
to PLUMED users
Hi Qinghua,
Already attached in the original post :)
Cheers,
Billy
Already attached in the original post :)
Cheers,
Billy
qingh...@gmail.com
Jan 15, 2018, 2:34:47 AM1/15/18
to PLUMED users
Hello Billy,
Thanks for it, I have it now!
All the best,
Qinghua
Thanks for it, I have it now!
All the best,
Qinghua
Billy Noonan
Dec 4, 2018, 3:43:52 AM12/4/18
to PLUMED users
Dear Gareth (And all other esteemed plumed users...),
I am trying to use this same method (as above) to bias the dynamics of a portion of a protein of interest. The error is at the end of this post, but I wanted to I am receiving an error when I go to print the eig1 and eig2 values across my unbiased trajectory
Relevant information here:
I get the following output:
Then when I run this with plumed driver:
I am trying to use this same method (as above) to bias the dynamics of a portion of a protein of interest. The error is at the end of this post, but I wanted to I am receiving an error when I go to print the eig1 and eig2 values across my unbiased trajectory
Relevant information here:
metadynamics.ndx:
[ minimal_binding_site ]
436 443 448 449 451 453 454 456 458 464 469 470 472 474 475
477 479 485 490 493 494 502 507 508 510 512 513 515 517 523
528 531 532 533 540 550 555 558 561 564 572 576 580 583 591
595 599 607 614 619 622 625 628 636 640 644 1485 1490 1559 1564
plumed-PCA.dat:
binding_site: GROUP NDX_FILE=metadynamics.ndx NDX_GROUP=minimal_binding_site
PCA METRIC=OPTIMAL ATOMS=binding_site STRIDE=1 NLOW_DIM=2 OFILE=pca-comp-1.pdb
When I run $ plumed driver --plumed plumed-PCA.dat --mf_xtc md_meta_2.xtc[ minimal_binding_site ]
436 443 448 449 451 453 454 456 458 464 469 470 472 474 475
477 479 485 490 493 494 502 507 508 510 512 513 515 517 523
528 531 532 533 540 550 555 558 561 564 572 576 580 583 591
595 599 607 614 619 622 625 628 636 640 644 1485 1490 1559 1564
plumed-PCA.dat:
binding_site: GROUP NDX_FILE=metadynamics.ndx NDX_GROUP=minimal_binding_site
PCA METRIC=OPTIMAL ATOMS=binding_site STRIDE=1 NLOW_DIM=2 OFILE=pca-comp-1.pdb
I get the following output:
pca-comp-1.pdb:
REMARK TYPE=OPTIMAL
ATOM 436 X RES 0 6.806 -7.007 10.293 0.02 0.02
ATOM 443 X RES 1 5.101 -5.467 7.258 0.02 0.02
ATOM 448 X RES 2 5.897 -7.174 5.593 0.02 0.02
ATOM 449 X RES 3 6.336 -8.185 6.055 0.02 0.02
ATOM 451 X RES 4 7.376 -8.865 5.549 0.02 0.02
ATOM 453 X RES 5 7.978 -8.539 4.561 0.02 0.02
ATOM 454 X RES 6 8.991 -9.188 4.070 0.02 0.02
ATOM 456 X RES 7 7.526 -7.536 4.084 0.02 0.02
ATOM 458 X RES 8 6.493 -6.855 4.606 0.02 0.02
ATOM 464 X RES 9 2.752 -2.552 6.623 0.02 0.02
ATOM 469 X RES 10 4.145 -0.474 7.183 0.02 0.02
ATOM 470 X RES 11 5.420 -0.723 7.632 0.02 0.02
ATOM 472 X RES 12 6.450 0.156 7.355 0.02 0.02
ATOM 474 X RES 13 6.202 1.300 6.623 0.02 0.02
ATOM 475 X RES 14 7.196 2.158 6.352 0.02 0.02
ATOM 477 X RES 15 4.921 1.542 6.162 0.02 0.02
ATOM 479 X RES 16 3.900 0.655 6.442 0.02 0.02
ATOM 485 X RES 17 0.705 -1.164 3.737 0.02 0.02
ATOM 490 X RES 18 -0.913 -2.717 2.981 0.02 0.02
ATOM 493 X RES 19 -2.016 -3.906 2.373 0.02 0.02
ATOM 494 X RES 20 -2.458 -3.399 1.120 0.02 0.02
ATOM 502 X RES 21 -0.367 2.350 2.807 0.02 0.02
ATOM 507 X RES 22 1.803 3.395 2.039 0.02 0.02
ATOM 508 X RES 23 2.012 4.120 2.315 0.02 0.02
ATOM 510 X RES 24 3.195 4.336 2.287 0.02 0.02
ATOM 512 X RES 25 4.175 3.825 1.969 0.02 0.02
ATOM 513 X RES 26 5.332 4.051 1.939 0.02 0.02
ATOM 515 X RES 27 3.956 3.088 1.687 0.02 0.02
ATOM 517 X RES 28 2.775 2.879 1.725 0.02 0.02
ATOM 523 X RES 29 -3.936 3.449 2.332 0.02 0.02
ATOM 528 X RES 30 -6.008 4.334 3.281 0.02 0.02
ATOM 531 X RES 31 -6.678 5.252 4.097 0.02 0.02
ATOM 532 X RES 32 -6.761 6.275 4.088 0.02 0.02
ATOM 533 X RES 33 -7.166 4.942 4.850 0.02 0.02
ATOM 540 X RES 34 -3.726 5.877 -0.557 0.02 0.02
ATOM 550 X RES 35 -1.953 3.458 -2.876 0.02 0.02
ATOM 555 X RES 36 0.394 4.195 -2.557 0.02 0.02
ATOM 558 X RES 37 0.926 4.693 -3.362 0.02 0.02
ATOM 561 X RES 38 1.822 5.526 -3.422 0.02 0.02
ATOM 564 X RES 39 2.400 5.963 -3.992 0.02 0.02
ATOM 572 X RES 40 -4.749 0.873 -2.945 0.02 0.02
ATOM 576 X RES 41 -6.384 -0.790 -2.146 0.02 0.02
ATOM 580 X RES 42 -4.557 -0.127 -0.648 0.02 0.02
ATOM 583 X RES 43 -5.181 -0.495 0.644 0.02 0.02
ATOM 591 X RES 44 -6.475 1.166 -6.329 0.02 0.02
ATOM 595 X RES 45 -5.591 3.076 -7.157 0.02 0.02
ATOM 599 X RES 46 -4.698 1.929 -7.625 0.02 0.02
ATOM 607 X RES 47 -8.745 -0.950 -8.480 0.02 0.02
ATOM 614 X RES 48 -9.681 -1.194 -12.132 0.02 0.02
ATOM 619 X RES 49 -7.978 -0.407 -13.344 0.02 0.02
ATOM 622 X RES 50 -7.121 0.102 -14.162 0.02 0.02
ATOM 625 X RES 51 -6.558 0.356 -14.481 0.02 0.02
ATOM 628 X RES 52 -5.953 0.790 -15.095 0.02 0.02
ATOM 636 X RES 53 -12.067 -3.380 -14.113 0.02 0.02
ATOM 640 X RES 54 -13.717 -3.478 -12.200 0.02 0.02
ATOM 644 X RES 55 -14.093 -2.086 -14.046 0.02 0.02
ATOM 1485 X RES 56 6.926 -1.797 3.220 0.02 0.02
ATOM 1490 X RES 57 6.980 0.936 2.535 0.02 0.02
ATOM 1559 X RES 58 9.859 -0.373 0.902 0.02 0.02
ATOM 1564 X RES 59 8.780 1.780 2.301 0.02 0.02
END
REMARK TYPE=DIRECTION
ATOM 436 X RES 0 0.213 -0.298 0.167 1.00 1.00
ATOM 443 X RES 1 0.202 -0.257 0.189 1.00 1.00
ATOM 448 X RES 2 0.408 -0.102 0.135 1.00 1.00
ATOM 449 X RES 3 0.485 0.314 -0.364 1.00 1.00
ATOM 451 X RES 4 0.549 0.405 -0.353 1.00 1.00
ATOM 453 X RES 5 0.545 0.085 0.168 1.00 1.00
ATOM 454 X RES 6 0.602 0.170 0.180 1.00 1.00
ATOM 456 X RES 7 0.479 -0.325 0.678 1.00 1.00
ATOM 458 X RES 8 0.407 -0.420 0.656 1.00 1.00
ATOM 464 X RES 9 -0.048 -0.438 0.309 1.00 1.00
ATOM 469 X RES 10 -0.299 -0.353 0.592 1.00 1.00
ATOM 470 X RES 11 -0.277 -0.264 0.599 1.00 1.00
ATOM 472 X RES 12 -0.371 -0.113 0.740 1.00 1.00
ATOM 474 X RES 13 -0.491 -0.053 0.874 1.00 1.00
ATOM 475 X RES 14 -0.590 0.101 1.009 1.00 1.00
ATOM 477 X RES 15 -0.512 -0.141 0.864 1.00 1.00
ATOM 479 X RES 16 -0.417 -0.291 0.726 1.00 1.00
ATOM 485 X RES 17 -0.045 -0.194 0.431 1.00 1.00
ATOM 490 X RES 18 0.408 -0.517 0.231 1.00 1.00
ATOM 493 X RES 19 0.319 -0.360 0.103 1.00 1.00
ATOM 494 X RES 20 0.386 -0.273 0.096 1.00 1.00
ATOM 502 X RES 21 -0.028 -0.069 0.940 1.00 1.00
ATOM 507 X RES 22 -0.205 -0.210 0.234 1.00 1.00
ATOM 508 X RES 23 -0.712 -0.115 -1.525 1.00 1.00
ATOM 510 X RES 24 -1.094 -0.312 -2.931 1.00 1.00
ATOM 512 X RES 25 -0.984 -0.635 -2.579 1.00 1.00
ATOM 513 X RES 26 -1.324 -0.817 -3.905 1.00 1.00
ATOM 515 X RES 27 -0.490 -0.753 -0.825 1.00 1.00
ATOM 517 X RES 28 -0.097 -0.527 0.578 1.00 1.00
ATOM 523 X RES 29 0.280 0.240 -0.001 1.00 1.00
ATOM 528 X RES 30 -0.059 0.260 -0.512 1.00 1.00
ATOM 531 X RES 31 -0.223 0.270 -0.469 1.00 1.00
ATOM 532 X RES 32 -0.286 0.321 -0.647 1.00 1.00
ATOM 533 X RES 33 -0.297 0.223 -0.223 1.00 1.00
ATOM 540 X RES 34 0.828 0.050 -0.098 1.00 1.00
ATOM 550 X RES 35 0.385 -0.253 -0.104 1.00 1.00
ATOM 555 X RES 36 0.463 -0.547 -0.918 1.00 1.00
ATOM 558 X RES 37 -0.354 -0.251 -1.743 1.00 1.00
ATOM 561 X RES 38 -0.307 -0.677 -2.488 1.00 1.00
ATOM 564 X RES 39 -0.414 -0.852 -2.812 1.00 1.00
ATOM 572 X RES 40 0.302 -0.163 0.362 1.00 1.00
ATOM 576 X RES 41 0.337 -0.075 0.603 1.00 1.00
ATOM 580 X RES 42 0.467 0.023 0.435 1.00 1.00
ATOM 583 X RES 43 0.548 0.065 0.497 1.00 1.00
ATOM 591 X RES 44 0.171 -0.178 0.428 1.00 1.00
ATOM 595 X RES 45 -0.029 -0.253 0.229 1.00 1.00
ATOM 599 X RES 46 0.013 0.140 0.540 1.00 1.00
ATOM 607 X RES 47 0.176 -0.167 0.415 1.00 1.00
ATOM 614 X RES 48 0.359 0.107 0.347 1.00 1.00
ATOM 619 X RES 49 0.313 0.987 0.855 1.00 1.00
ATOM 622 X RES 50 0.061 1.216 0.989 1.00 1.00
ATOM 625 X RES 51 -0.006 1.936 1.327 1.00 1.00
ATOM 628 X RES 52 -0.251 2.227 1.492 1.00 1.00
ATOM 636 X RES 53 0.505 0.180 0.098 1.00 1.00
ATOM 640 X RES 54 0.449 0.032 0.043 1.00 1.00
ATOM 644 X RES 55 0.476 0.133 0.117 1.00 1.00
ATOM 1485 X RES 56 -0.002 0.291 0.648 1.00 1.00
ATOM 1490 X RES 57 -0.374 0.349 0.856 1.00 1.00
ATOM 1559 X RES 58 -0.132 0.650 0.817 1.00 1.00
ATOM 1564 X RES 59 -0.420 0.477 0.900 1.00 1.00
END
REMARK TYPE=DIRECTION
ATOM 436 X RES 0 0.227 -0.621 -0.482 1.00 1.00
ATOM 443 X RES 1 -0.001 -0.333 -0.202 1.00 1.00
ATOM 448 X RES 2 -0.183 0.103 -0.703 1.00 1.00
ATOM 449 X RES 3 0.062 0.236 -1.249 1.00 1.00
ATOM 451 X RES 4 -0.029 0.475 -1.693 1.00 1.00
ATOM 453 X RES 5 -0.363 0.590 -1.576 1.00 1.00
ATOM 454 X RES 6 -0.474 0.809 -2.024 1.00 1.00
ATOM 456 X RES 7 -0.592 0.475 -1.008 1.00 1.00
ATOM 458 X RES 8 -0.503 0.230 -0.574 1.00 1.00
ATOM 464 X RES 9 -0.022 -0.269 0.245 1.00 1.00
ATOM 469 X RES 10 -0.074 -0.291 0.436 1.00 1.00
ATOM 470 X RES 11 -0.055 -0.301 0.384 1.00 1.00
ATOM 472 X RES 12 -0.090 -0.237 0.460 1.00 1.00
ATOM 474 X RES 13 -0.145 -0.168 0.589 1.00 1.00
ATOM 475 X RES 14 -0.182 -0.104 0.659 1.00 1.00
ATOM 477 X RES 15 -0.164 -0.160 0.636 1.00 1.00
ATOM 479 X RES 16 -0.130 -0.221 0.562 1.00 1.00
ATOM 485 X RES 17 -0.091 -0.007 0.423 1.00 1.00
ATOM 490 X RES 18 -0.084 0.093 0.242 1.00 1.00
ATOM 493 X RES 19 -0.147 0.170 0.214 1.00 1.00
ATOM 494 X RES 20 -0.094 0.136 0.260 1.00 1.00
ATOM 502 X RES 21 -0.027 0.105 0.807 1.00 1.00
ATOM 507 X RES 22 -0.117 0.023 0.439 1.00 1.00
ATOM 508 X RES 23 -0.340 0.053 -0.393 1.00 1.00
ATOM 510 X RES 24 -0.516 -0.056 -1.085 1.00 1.00
ATOM 512 X RES 25 -0.479 -0.212 -0.945 1.00 1.00
ATOM 513 X RES 26 -0.637 -0.303 -1.606 1.00 1.00
ATOM 515 X RES 27 -0.263 -0.257 -0.112 1.00 1.00
ATOM 517 X RES 28 -0.082 -0.134 0.576 1.00 1.00
ATOM 523 X RES 29 0.129 0.347 0.519 1.00 1.00
ATOM 528 X RES 30 0.139 0.321 0.490 1.00 1.00
ATOM 531 X RES 31 0.078 0.268 0.702 1.00 1.00
ATOM 532 X RES 32 -0.019 0.288 0.601 1.00 1.00
ATOM 533 X RES 33 0.137 0.198 1.009 1.00 1.00
ATOM 540 X RES 34 0.318 0.349 0.549 1.00 1.00
ATOM 550 X RES 35 0.030 0.289 0.397 1.00 1.00
ATOM 555 X RES 36 0.071 0.177 0.031 1.00 1.00
ATOM 558 X RES 37 -0.286 0.318 -0.263 1.00 1.00
ATOM 561 X RES 38 -0.264 0.162 -0.565 1.00 1.00
ATOM 564 X RES 39 -0.341 0.118 -0.705 1.00 1.00
ATOM 572 X RES 40 -0.028 0.359 0.544 1.00 1.00
ATOM 576 X RES 41 -0.010 0.395 0.623 1.00 1.00
ATOM 580 X RES 42 0.047 0.361 0.529 1.00 1.00
ATOM 583 X RES 43 0.101 0.337 0.530 1.00 1.00
ATOM 591 X RES 44 -0.096 0.546 0.595 1.00 1.00
ATOM 595 X RES 45 0.143 0.906 1.192 1.00 1.00
ATOM 599 X RES 46 0.070 0.183 0.392 1.00 1.00
ATOM 607 X RES 47 0.007 0.737 0.279 1.00 1.00
ATOM 614 X RES 48 0.034 0.792 0.273 1.00 1.00
ATOM 619 X RES 49 0.478 -1.350 -0.431 1.00 1.00
ATOM 622 X RES 50 1.359 -1.823 -0.586 1.00 1.00
ATOM 625 X RES 51 1.802 -3.867 -1.095 1.00 1.00
ATOM 628 X RES 52 2.722 -4.540 -1.466 1.00 1.00
ATOM 636 X RES 53 -0.182 1.002 0.290 1.00 1.00
ATOM 640 X RES 54 -0.133 1.029 0.332 1.00 1.00
ATOM 644 X RES 55 -0.109 1.116 0.394 1.00 1.00
ATOM 1485 X RES 56 -0.065 0.212 0.297 1.00 1.00
ATOM 1490 X RES 57 -0.186 0.250 0.465 1.00 1.00
ATOM 1559 X RES 58 -0.151 0.400 0.327 1.00 1.00
ATOM 1564 X RES 59 -0.199 0.295 0.474 1.00 1.00
END
REMARK TYPE=OPTIMAL
ATOM 436 X RES 0 6.806 -7.007 10.293 0.02 0.02
ATOM 443 X RES 1 5.101 -5.467 7.258 0.02 0.02
ATOM 448 X RES 2 5.897 -7.174 5.593 0.02 0.02
ATOM 449 X RES 3 6.336 -8.185 6.055 0.02 0.02
ATOM 451 X RES 4 7.376 -8.865 5.549 0.02 0.02
ATOM 453 X RES 5 7.978 -8.539 4.561 0.02 0.02
ATOM 454 X RES 6 8.991 -9.188 4.070 0.02 0.02
ATOM 456 X RES 7 7.526 -7.536 4.084 0.02 0.02
ATOM 458 X RES 8 6.493 -6.855 4.606 0.02 0.02
ATOM 464 X RES 9 2.752 -2.552 6.623 0.02 0.02
ATOM 469 X RES 10 4.145 -0.474 7.183 0.02 0.02
ATOM 470 X RES 11 5.420 -0.723 7.632 0.02 0.02
ATOM 472 X RES 12 6.450 0.156 7.355 0.02 0.02
ATOM 474 X RES 13 6.202 1.300 6.623 0.02 0.02
ATOM 475 X RES 14 7.196 2.158 6.352 0.02 0.02
ATOM 477 X RES 15 4.921 1.542 6.162 0.02 0.02
ATOM 479 X RES 16 3.900 0.655 6.442 0.02 0.02
ATOM 485 X RES 17 0.705 -1.164 3.737 0.02 0.02
ATOM 490 X RES 18 -0.913 -2.717 2.981 0.02 0.02
ATOM 493 X RES 19 -2.016 -3.906 2.373 0.02 0.02
ATOM 494 X RES 20 -2.458 -3.399 1.120 0.02 0.02
ATOM 502 X RES 21 -0.367 2.350 2.807 0.02 0.02
ATOM 507 X RES 22 1.803 3.395 2.039 0.02 0.02
ATOM 508 X RES 23 2.012 4.120 2.315 0.02 0.02
ATOM 510 X RES 24 3.195 4.336 2.287 0.02 0.02
ATOM 512 X RES 25 4.175 3.825 1.969 0.02 0.02
ATOM 513 X RES 26 5.332 4.051 1.939 0.02 0.02
ATOM 515 X RES 27 3.956 3.088 1.687 0.02 0.02
ATOM 517 X RES 28 2.775 2.879 1.725 0.02 0.02
ATOM 523 X RES 29 -3.936 3.449 2.332 0.02 0.02
ATOM 528 X RES 30 -6.008 4.334 3.281 0.02 0.02
ATOM 531 X RES 31 -6.678 5.252 4.097 0.02 0.02
ATOM 532 X RES 32 -6.761 6.275 4.088 0.02 0.02
ATOM 533 X RES 33 -7.166 4.942 4.850 0.02 0.02
ATOM 540 X RES 34 -3.726 5.877 -0.557 0.02 0.02
ATOM 550 X RES 35 -1.953 3.458 -2.876 0.02 0.02
ATOM 555 X RES 36 0.394 4.195 -2.557 0.02 0.02
ATOM 558 X RES 37 0.926 4.693 -3.362 0.02 0.02
ATOM 561 X RES 38 1.822 5.526 -3.422 0.02 0.02
ATOM 564 X RES 39 2.400 5.963 -3.992 0.02 0.02
ATOM 572 X RES 40 -4.749 0.873 -2.945 0.02 0.02
ATOM 576 X RES 41 -6.384 -0.790 -2.146 0.02 0.02
ATOM 580 X RES 42 -4.557 -0.127 -0.648 0.02 0.02
ATOM 583 X RES 43 -5.181 -0.495 0.644 0.02 0.02
ATOM 591 X RES 44 -6.475 1.166 -6.329 0.02 0.02
ATOM 595 X RES 45 -5.591 3.076 -7.157 0.02 0.02
ATOM 599 X RES 46 -4.698 1.929 -7.625 0.02 0.02
ATOM 607 X RES 47 -8.745 -0.950 -8.480 0.02 0.02
ATOM 614 X RES 48 -9.681 -1.194 -12.132 0.02 0.02
ATOM 619 X RES 49 -7.978 -0.407 -13.344 0.02 0.02
ATOM 622 X RES 50 -7.121 0.102 -14.162 0.02 0.02
ATOM 625 X RES 51 -6.558 0.356 -14.481 0.02 0.02
ATOM 628 X RES 52 -5.953 0.790 -15.095 0.02 0.02
ATOM 636 X RES 53 -12.067 -3.380 -14.113 0.02 0.02
ATOM 640 X RES 54 -13.717 -3.478 -12.200 0.02 0.02
ATOM 644 X RES 55 -14.093 -2.086 -14.046 0.02 0.02
ATOM 1485 X RES 56 6.926 -1.797 3.220 0.02 0.02
ATOM 1490 X RES 57 6.980 0.936 2.535 0.02 0.02
ATOM 1559 X RES 58 9.859 -0.373 0.902 0.02 0.02
ATOM 1564 X RES 59 8.780 1.780 2.301 0.02 0.02
END
REMARK TYPE=DIRECTION
ATOM 436 X RES 0 0.213 -0.298 0.167 1.00 1.00
ATOM 443 X RES 1 0.202 -0.257 0.189 1.00 1.00
ATOM 448 X RES 2 0.408 -0.102 0.135 1.00 1.00
ATOM 449 X RES 3 0.485 0.314 -0.364 1.00 1.00
ATOM 451 X RES 4 0.549 0.405 -0.353 1.00 1.00
ATOM 453 X RES 5 0.545 0.085 0.168 1.00 1.00
ATOM 454 X RES 6 0.602 0.170 0.180 1.00 1.00
ATOM 456 X RES 7 0.479 -0.325 0.678 1.00 1.00
ATOM 458 X RES 8 0.407 -0.420 0.656 1.00 1.00
ATOM 464 X RES 9 -0.048 -0.438 0.309 1.00 1.00
ATOM 469 X RES 10 -0.299 -0.353 0.592 1.00 1.00
ATOM 470 X RES 11 -0.277 -0.264 0.599 1.00 1.00
ATOM 472 X RES 12 -0.371 -0.113 0.740 1.00 1.00
ATOM 474 X RES 13 -0.491 -0.053 0.874 1.00 1.00
ATOM 475 X RES 14 -0.590 0.101 1.009 1.00 1.00
ATOM 477 X RES 15 -0.512 -0.141 0.864 1.00 1.00
ATOM 479 X RES 16 -0.417 -0.291 0.726 1.00 1.00
ATOM 485 X RES 17 -0.045 -0.194 0.431 1.00 1.00
ATOM 490 X RES 18 0.408 -0.517 0.231 1.00 1.00
ATOM 493 X RES 19 0.319 -0.360 0.103 1.00 1.00
ATOM 494 X RES 20 0.386 -0.273 0.096 1.00 1.00
ATOM 502 X RES 21 -0.028 -0.069 0.940 1.00 1.00
ATOM 507 X RES 22 -0.205 -0.210 0.234 1.00 1.00
ATOM 508 X RES 23 -0.712 -0.115 -1.525 1.00 1.00
ATOM 510 X RES 24 -1.094 -0.312 -2.931 1.00 1.00
ATOM 512 X RES 25 -0.984 -0.635 -2.579 1.00 1.00
ATOM 513 X RES 26 -1.324 -0.817 -3.905 1.00 1.00
ATOM 515 X RES 27 -0.490 -0.753 -0.825 1.00 1.00
ATOM 517 X RES 28 -0.097 -0.527 0.578 1.00 1.00
ATOM 523 X RES 29 0.280 0.240 -0.001 1.00 1.00
ATOM 528 X RES 30 -0.059 0.260 -0.512 1.00 1.00
ATOM 531 X RES 31 -0.223 0.270 -0.469 1.00 1.00
ATOM 532 X RES 32 -0.286 0.321 -0.647 1.00 1.00
ATOM 533 X RES 33 -0.297 0.223 -0.223 1.00 1.00
ATOM 540 X RES 34 0.828 0.050 -0.098 1.00 1.00
ATOM 550 X RES 35 0.385 -0.253 -0.104 1.00 1.00
ATOM 555 X RES 36 0.463 -0.547 -0.918 1.00 1.00
ATOM 558 X RES 37 -0.354 -0.251 -1.743 1.00 1.00
ATOM 561 X RES 38 -0.307 -0.677 -2.488 1.00 1.00
ATOM 564 X RES 39 -0.414 -0.852 -2.812 1.00 1.00
ATOM 572 X RES 40 0.302 -0.163 0.362 1.00 1.00
ATOM 576 X RES 41 0.337 -0.075 0.603 1.00 1.00
ATOM 580 X RES 42 0.467 0.023 0.435 1.00 1.00
ATOM 583 X RES 43 0.548 0.065 0.497 1.00 1.00
ATOM 591 X RES 44 0.171 -0.178 0.428 1.00 1.00
ATOM 595 X RES 45 -0.029 -0.253 0.229 1.00 1.00
ATOM 599 X RES 46 0.013 0.140 0.540 1.00 1.00
ATOM 607 X RES 47 0.176 -0.167 0.415 1.00 1.00
ATOM 614 X RES 48 0.359 0.107 0.347 1.00 1.00
ATOM 619 X RES 49 0.313 0.987 0.855 1.00 1.00
ATOM 622 X RES 50 0.061 1.216 0.989 1.00 1.00
ATOM 625 X RES 51 -0.006 1.936 1.327 1.00 1.00
ATOM 628 X RES 52 -0.251 2.227 1.492 1.00 1.00
ATOM 636 X RES 53 0.505 0.180 0.098 1.00 1.00
ATOM 640 X RES 54 0.449 0.032 0.043 1.00 1.00
ATOM 644 X RES 55 0.476 0.133 0.117 1.00 1.00
ATOM 1485 X RES 56 -0.002 0.291 0.648 1.00 1.00
ATOM 1490 X RES 57 -0.374 0.349 0.856 1.00 1.00
ATOM 1559 X RES 58 -0.132 0.650 0.817 1.00 1.00
ATOM 1564 X RES 59 -0.420 0.477 0.900 1.00 1.00
END
REMARK TYPE=DIRECTION
ATOM 436 X RES 0 0.227 -0.621 -0.482 1.00 1.00
ATOM 443 X RES 1 -0.001 -0.333 -0.202 1.00 1.00
ATOM 448 X RES 2 -0.183 0.103 -0.703 1.00 1.00
ATOM 449 X RES 3 0.062 0.236 -1.249 1.00 1.00
ATOM 451 X RES 4 -0.029 0.475 -1.693 1.00 1.00
ATOM 453 X RES 5 -0.363 0.590 -1.576 1.00 1.00
ATOM 454 X RES 6 -0.474 0.809 -2.024 1.00 1.00
ATOM 456 X RES 7 -0.592 0.475 -1.008 1.00 1.00
ATOM 458 X RES 8 -0.503 0.230 -0.574 1.00 1.00
ATOM 464 X RES 9 -0.022 -0.269 0.245 1.00 1.00
ATOM 469 X RES 10 -0.074 -0.291 0.436 1.00 1.00
ATOM 470 X RES 11 -0.055 -0.301 0.384 1.00 1.00
ATOM 472 X RES 12 -0.090 -0.237 0.460 1.00 1.00
ATOM 474 X RES 13 -0.145 -0.168 0.589 1.00 1.00
ATOM 475 X RES 14 -0.182 -0.104 0.659 1.00 1.00
ATOM 477 X RES 15 -0.164 -0.160 0.636 1.00 1.00
ATOM 479 X RES 16 -0.130 -0.221 0.562 1.00 1.00
ATOM 485 X RES 17 -0.091 -0.007 0.423 1.00 1.00
ATOM 490 X RES 18 -0.084 0.093 0.242 1.00 1.00
ATOM 493 X RES 19 -0.147 0.170 0.214 1.00 1.00
ATOM 494 X RES 20 -0.094 0.136 0.260 1.00 1.00
ATOM 502 X RES 21 -0.027 0.105 0.807 1.00 1.00
ATOM 507 X RES 22 -0.117 0.023 0.439 1.00 1.00
ATOM 508 X RES 23 -0.340 0.053 -0.393 1.00 1.00
ATOM 510 X RES 24 -0.516 -0.056 -1.085 1.00 1.00
ATOM 512 X RES 25 -0.479 -0.212 -0.945 1.00 1.00
ATOM 513 X RES 26 -0.637 -0.303 -1.606 1.00 1.00
ATOM 515 X RES 27 -0.263 -0.257 -0.112 1.00 1.00
ATOM 517 X RES 28 -0.082 -0.134 0.576 1.00 1.00
ATOM 523 X RES 29 0.129 0.347 0.519 1.00 1.00
ATOM 528 X RES 30 0.139 0.321 0.490 1.00 1.00
ATOM 531 X RES 31 0.078 0.268 0.702 1.00 1.00
ATOM 532 X RES 32 -0.019 0.288 0.601 1.00 1.00
ATOM 533 X RES 33 0.137 0.198 1.009 1.00 1.00
ATOM 540 X RES 34 0.318 0.349 0.549 1.00 1.00
ATOM 550 X RES 35 0.030 0.289 0.397 1.00 1.00
ATOM 555 X RES 36 0.071 0.177 0.031 1.00 1.00
ATOM 558 X RES 37 -0.286 0.318 -0.263 1.00 1.00
ATOM 561 X RES 38 -0.264 0.162 -0.565 1.00 1.00
ATOM 564 X RES 39 -0.341 0.118 -0.705 1.00 1.00
ATOM 572 X RES 40 -0.028 0.359 0.544 1.00 1.00
ATOM 576 X RES 41 -0.010 0.395 0.623 1.00 1.00
ATOM 580 X RES 42 0.047 0.361 0.529 1.00 1.00
ATOM 583 X RES 43 0.101 0.337 0.530 1.00 1.00
ATOM 591 X RES 44 -0.096 0.546 0.595 1.00 1.00
ATOM 595 X RES 45 0.143 0.906 1.192 1.00 1.00
ATOM 599 X RES 46 0.070 0.183 0.392 1.00 1.00
ATOM 607 X RES 47 0.007 0.737 0.279 1.00 1.00
ATOM 614 X RES 48 0.034 0.792 0.273 1.00 1.00
ATOM 619 X RES 49 0.478 -1.350 -0.431 1.00 1.00
ATOM 622 X RES 50 1.359 -1.823 -0.586 1.00 1.00
ATOM 625 X RES 51 1.802 -3.867 -1.095 1.00 1.00
ATOM 628 X RES 52 2.722 -4.540 -1.466 1.00 1.00
ATOM 636 X RES 53 -0.182 1.002 0.290 1.00 1.00
ATOM 640 X RES 54 -0.133 1.029 0.332 1.00 1.00
ATOM 644 X RES 55 -0.109 1.116 0.394 1.00 1.00
ATOM 1485 X RES 56 -0.065 0.212 0.297 1.00 1.00
ATOM 1490 X RES 57 -0.186 0.250 0.465 1.00 1.00
ATOM 1559 X RES 58 -0.151 0.400 0.327 1.00 1.00
ATOM 1564 X RES 59 -0.199 0.295 0.474 1.00 1.00
END
Then when I run this with plumed driver:
plumed-print-PCA.dat:
pca2: PCAVARS REFERENCE=pca-comp-1.pdb TYPE=OPTIMAL
PRINT ARG=pca2.eig-1,pca2.eig-2 FILE=PCA-values-unbiased.dat
This is error is printed to the terminal:pca2: PCAVARS REFERENCE=pca-comp-1.pdb TYPE=OPTIMAL
PRINT ARG=pca2.eig-1,pca2.eig-2 FILE=PCA-values-unbiased.dat
plumed driver --plumed plumed-print-PCA.dat --mf_xtc md_meta_2.xtc
DRIVER: Found molfile format trajectory xtc with name md_meta_2.xtc
PLUMED: PLUMED is starting
PLUMED: Version: 2.4.1 (git: Unknown) compiled on Mar 12 2018 at 16:29:58
PLUMED: Please cite this paper when using PLUMED [1]
PLUMED: For further information see the PLUMED web page at http://www.plumed.org
PLUMED: Root: /apps/linux/plumed/plumed-2.4.1/lib64/plumed
PLUMED: For installed feature, see /apps/linux/plumed/plumed-2.4.1/lib64/plumed/src/config/config.txt
PLUMED: Molecular dynamics engine: driver
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 1692
PLUMED: File suffix:
PLUMED: FILE: plumed-print-PCA.dat
PLUMED: Action PCAVARS
PLUMED: with label pca2
PLUMED: found 2 eigenvectors in file pca-comp-1.pdb
PLUMED: ERROR in input to action PCAVARS with label pca2 : atom out of range
PLUMED:
terminate called after throwing an instance of 'PLMD::Exception'
what():
+++ Internal PLUMED error
+++ file Action.cpp, line 242
+++ message: ERROR in input to action PCAVARS with label pca2 : atom out of range
[alpha:104819] *** Process received signal ***
[alpha:104819] Signal: Aborted (6)
[alpha:104819] Signal code: (-6)
[alpha:104819] [ 0] /lib64/libpthread.so.0(+0x122e0)[0x2af444d242e0]
[alpha:104819] [ 1] /lib64/libc.so.6(gsignal+0x110)[0x2af444f660e0]
[alpha:104819] [ 2] /lib64/libc.so.6(abort+0x151)[0x2af444f676c1]
[alpha:104819] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x125)[0x2af44302e485]
[alpha:104819] [ 4] /usr/lib64/libstdc++.so.6(+0x97276)[0x2af44302c276]
[alpha:104819] [ 5] /usr/lib64/libstdc++.so.6(+0x972c1)[0x2af44302c2c1]
[alpha:104819] [ 6] /usr/lib64/libstdc++.so.6(+0x97503)[0x2af44302c503]
[alpha:104819] [ 7] plumed(_ZNK4PLMD6Action5errorERKSs+0x206)[0x601ad6]
[alpha:104819] [ 8] plumed(_ZN4PLMD15ActionAtomistic12requestAtomsERKSt6vectorINS_10AtomNumberESaIS2_EE+0x235)[0x5fe375]
[alpha:104819] [ 9] plumed(_ZN4PLMD7mapping7PCAVarsC1ERKNS_13ActionOptionsE+0xb7d)[0x79e96d]
[alpha:104819] [10] plumed(_ZN4PLMD7mapping20PCAVarsRegisterMe1966createERKNS_13ActionOptionsE+0x21)[0x7a0b11]
[alpha:104819] [11] plumed(_ZN4PLMD14ActionRegister6createERKNS_13ActionOptionsE+0x526)[0x6067a6]
[alpha:104819] [12] plumed(_ZN4PLMD10PlumedMain14readInputWordsERKSt6vectorISsSaISsEE+0x286)[0x63f136]
[alpha:104819] [13] plumed(_ZN4PLMD10PlumedMain13readInputFileESs+0xa8)[0x63fc08]
[alpha:104819] [14] plumed(_ZN4PLMD10PlumedMain4initEv+0xd57)[0x640d17]
[alpha:104819] [15] plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x54e)[0x6423ce]
[alpha:104819] [16] plumed(plumedmain_cmd+0x36)[0x64e306]
[alpha:104819] [17] plumed(_ZN4PLMD7cltools6DriverIdE4mainEP8_IO_FILES4_RNS_12CommunicatorE+0x2938)[0x4c0218]
[alpha:104819] [18] plumed(_ZN4PLMD10CLToolMain3runEiPPcP8_IO_FILES4_RNS_12CommunicatorE+0x6aa)[0x623b2a]
[alpha:104819] [19] plumed(_ZN4PLMD10CLToolMain3cmdERKSsPv+0x2e9)[0x6266c9]
[alpha:104819] [20] plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x4c8)[0x642348]
[alpha:104819] [21] plumed(plumedmain_cmd+0x36)[0x64e306]
[alpha:104819] [22] plumed(main+0x131)[0x4bc7a1]
[alpha:104819] [23] /lib64/libc.so.6(__libc_start_main+0xea)[0x2af444f50f4a]
[alpha:104819] [24] plumed(_start+0x29)[0x4e16f9]
[alpha:104819] *** End of error message ***
Abort (core dumped)
How do I fix this? What am I doing wrong? Does the PCA analysis have to start from atom 1 to be useable? I do not understand the errorDRIVER: Found molfile format trajectory xtc with name md_meta_2.xtc
PLUMED: PLUMED is starting
PLUMED: Version: 2.4.1 (git: Unknown) compiled on Mar 12 2018 at 16:29:58
PLUMED: Please cite this paper when using PLUMED [1]
PLUMED: For further information see the PLUMED web page at http://www.plumed.org
PLUMED: Root: /apps/linux/plumed/plumed-2.4.1/lib64/plumed
PLUMED: For installed feature, see /apps/linux/plumed/plumed-2.4.1/lib64/plumed/src/config/config.txt
PLUMED: Molecular dynamics engine: driver
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 1692
PLUMED: File suffix:
PLUMED: FILE: plumed-print-PCA.dat
PLUMED: Action PCAVARS
PLUMED: with label pca2
PLUMED: found 2 eigenvectors in file pca-comp-1.pdb
PLUMED: ERROR in input to action PCAVARS with label pca2 : atom out of range
PLUMED:
terminate called after throwing an instance of 'PLMD::Exception'
what():
+++ Internal PLUMED error
+++ file Action.cpp, line 242
+++ message: ERROR in input to action PCAVARS with label pca2 : atom out of range
[alpha:104819] *** Process received signal ***
[alpha:104819] Signal: Aborted (6)
[alpha:104819] Signal code: (-6)
[alpha:104819] [ 0] /lib64/libpthread.so.0(+0x122e0)[0x2af444d242e0]
[alpha:104819] [ 1] /lib64/libc.so.6(gsignal+0x110)[0x2af444f660e0]
[alpha:104819] [ 2] /lib64/libc.so.6(abort+0x151)[0x2af444f676c1]
[alpha:104819] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x125)[0x2af44302e485]
[alpha:104819] [ 4] /usr/lib64/libstdc++.so.6(+0x97276)[0x2af44302c276]
[alpha:104819] [ 5] /usr/lib64/libstdc++.so.6(+0x972c1)[0x2af44302c2c1]
[alpha:104819] [ 6] /usr/lib64/libstdc++.so.6(+0x97503)[0x2af44302c503]
[alpha:104819] [ 7] plumed(_ZNK4PLMD6Action5errorERKSs+0x206)[0x601ad6]
[alpha:104819] [ 8] plumed(_ZN4PLMD15ActionAtomistic12requestAtomsERKSt6vectorINS_10AtomNumberESaIS2_EE+0x235)[0x5fe375]
[alpha:104819] [ 9] plumed(_ZN4PLMD7mapping7PCAVarsC1ERKNS_13ActionOptionsE+0xb7d)[0x79e96d]
[alpha:104819] [10] plumed(_ZN4PLMD7mapping20PCAVarsRegisterMe1966createERKNS_13ActionOptionsE+0x21)[0x7a0b11]
[alpha:104819] [11] plumed(_ZN4PLMD14ActionRegister6createERKNS_13ActionOptionsE+0x526)[0x6067a6]
[alpha:104819] [12] plumed(_ZN4PLMD10PlumedMain14readInputWordsERKSt6vectorISsSaISsEE+0x286)[0x63f136]
[alpha:104819] [13] plumed(_ZN4PLMD10PlumedMain13readInputFileESs+0xa8)[0x63fc08]
[alpha:104819] [14] plumed(_ZN4PLMD10PlumedMain4initEv+0xd57)[0x640d17]
[alpha:104819] [15] plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x54e)[0x6423ce]
[alpha:104819] [16] plumed(plumedmain_cmd+0x36)[0x64e306]
[alpha:104819] [17] plumed(_ZN4PLMD7cltools6DriverIdE4mainEP8_IO_FILES4_RNS_12CommunicatorE+0x2938)[0x4c0218]
[alpha:104819] [18] plumed(_ZN4PLMD10CLToolMain3runEiPPcP8_IO_FILES4_RNS_12CommunicatorE+0x6aa)[0x623b2a]
[alpha:104819] [19] plumed(_ZN4PLMD10CLToolMain3cmdERKSsPv+0x2e9)[0x6266c9]
[alpha:104819] [20] plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x4c8)[0x642348]
[alpha:104819] [21] plumed(plumedmain_cmd+0x36)[0x64e306]
[alpha:104819] [22] plumed(main+0x131)[0x4bc7a1]
[alpha:104819] [23] /lib64/libc.so.6(__libc_start_main+0xea)[0x2af444f50f4a]
[alpha:104819] [24] plumed(_start+0x29)[0x4e16f9]
[alpha:104819] *** End of error message ***
Abort (core dumped)
Cheers,
Billy
On Wednesday, December 20, 2017 at 5:09:38 AM UTC+11, Gareth Tribello wrote:
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