Action: PCARMSD
| Module | colvar |
|---|---|
| Description | Usage |
| Calculate the PCA components for a number of provided eigenvectors and an average structure. |   |
Output components
This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.
| Name | Type | Description |
|---|---|---|
| eig | scalar | the projections on each eigenvalue are stored on values labeled eig-1, eig-2, |
| residual | scalar | the distance of the present configuration from the configuration supplied as AVERAGE in terms of mean squared displacement after optimal alignment |
Further details and examples
Calculate the PCA components for a number of provided eigenvectors and an average structure.
Information about this method can be found in the reference papers in the bibliography below. An example input is provided below:
Click on the labels of the actions for more information on what each action computes
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#SETTINGS INPUTFILES=regtest/trajectories/pca/average.pdb,regtest/trajectories/pca/eigenvec.pdb PCARMSDCalculate the PCA components for a number of provided eigenvectors and an average structure. More details ... AVERAGEa file in pdb format containing the reference structure and the atoms involved in the CV=regtest/trajectories/pca/average.pdbClick here to see an extract from this file.EIGENVECTORSa file in pdb format containing the reference structure and the atoms involved in the CV=×FILE: regtest/trajectories/pca/average.pdb
TITLE Average structure MODEL 1 ATOM 1 CL ALA 1 1.042 -3.070 0.946 1.00 0.00 ATOM 5 CLP ALA 1 0.416 -2.033 0.132 1.00 0.00 ATOM 6 OL ALA 1 0.415 -2.082 -0.976 1.00 0.00 ATOM 7 NL ALA 1 -0.134 -1.045 0.677 1.00 0.00 ATOM 9 CA ALA 1 -0.774 0.053 0.003 1.00 0.00 ATOM 10 HA ALA 1 -0.849 -0.166 -1.034 1.00 0.00 ATOM 11 CB ALA 1 -2.176 0.260 0.563 1.00 0.00 ATOM 15 CRP ALA 1 0.043 1.327 0.133 1.00 0.00 ATOM 16 OR ALA 1 0.314 1.825 0.962 1.00 0.00 ATOM 17 NR ALA 1 0.460 1.870 -0.708 1.00 0.00 ATOM 19 CR ALA 1 1.243 3.060 -0.699 1.00 0.00 TER ENDMDLregtest/trajectories/pca/eigenvec.pdbClick here to see an extract from this file....×FILE: regtest/trajectories/pca/eigenvec.pdb
TITLE frame t= -1.000 MODEL 1 ATOM 1 CL ALA 1 1.194 -2.988 0.724 1.00 0.00 ATOM 5 CLP ALA 1 -0.996 0.042 0.144 1.00 0.00 ATOM 6 OL ALA 1 -1.246 -0.178 -0.886 1.00 0.00 ATOM 7 NL ALA 1 -2.296 0.272 0.934 1.00 0.00 ATOM 9 CA ALA 1 -0.436 2.292 0.814 1.00 0.00 ATOM 10 HA ALA 1 0.944 1.312 -0.656 1.00 0.00 ATOM 11 CB ALA 1 1.824 2.452 -0.786 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 1 ATOM 1 CL ALA 1 1.042 -3.070 0.946 1.00 0.00 ATOM 5 CLP ALA 1 -0.774 0.053 0.003 1.00 0.00 ATOM 6 OL ALA 1 -0.849 -0.166 -1.034 1.00 0.00 ATOM 7 NL ALA 1 -2.176 0.260 0.563 1.00 0.00 ATOM 9 CA ALA 1 0.314 1.825 0.962 1.00 0.00 ATOM 10 HA ALA 1 0.460 1.870 -0.708 1.00 0.00 ATOM 11 CB ALA 1 1.243 3.060 -0.699 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 -0.000 -0.000 0.000 1.00 0.00 ATOM 19 CR ALA 1 0.000 -0.000 -0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.025 MODEL 1 ATOM 1 CL ALA 1 -0.622 -0.464 1.019 1.00 0.00 ATOM 5 CLP ALA 1 1.347 0.046 -0.807 1.00 0.00 ATOM 6 OL ALA 1 2.244 0.001 -0.850 1.00 0.00 ATOM 7 NL ALA 1 0.910 -0.181 -1.832 1.00 0.00 ATOM 9 CA ALA 1 4.148 -2.225 -0.203 1.00 0.00 ATOM 10 HA ALA 1 -2.701 2.896 0.404 1.00 0.00 ATOM 11 CB ALA 1 -3.385 3.314 1.083 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.003 MODEL 2 ATOM 1 CL ALA 1 1.406 0.307 -1.539 1.00 0.00 ATOM 5 CLP ALA 1 0.231 0.022 0.138 1.00 0.00 ATOM 6 OL ALA 1 -1.098 -0.164 0.397 1.00 0.00 ATOM 7 NL ALA 1 1.091 -0.485 2.080 1.00 0.00 ATOM 9 CA ALA 1 -0.757 1.408 -6.621 1.00 0.00 ATOM 10 HA ALA 1 0.399 -0.629 3.855 1.00 0.00 ATOM 11 CB ALA 1 0.285 -0.598 3.527 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.001 MODEL 3 ATOM 1 CL ALA 1 0.785 0.199 0.053 1.00 0.00 ATOM 5 CLP ALA 1 1.248 0.072 -0.329 1.00 0.00 ATOM 6 OL ALA 1 2.432 0.385 -0.373 1.00 0.00 ATOM 7 NL ALA 1 0.627 -1.884 -1.299 1.00 0.00 ATOM 9 CA ALA 1 -4.346 3.174 2.960 1.00 0.00 ATOM 10 HA ALA 1 2.210 -0.530 -1.054 1.00 0.00 ATOM 11 CB ALA 1 1.072 0.061 -0.500 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.001 MODEL 4 ATOM 1 CL ALA 1 5.360 4.442 0.605 1.00 0.00 ATOM 5 CLP ALA 1 -1.686 0.120 -0.761 1.00 0.00 ATOM 6 OL ALA 1 -1.774 0.228 -0.933 1.00 0.00 ATOM 7 NL ALA 1 -1.705 1.041 -0.655 1.00 0.00 ATOM 9 CA ALA 1 1.737 -2.971 1.580 1.00 0.00 ATOM 10 HA ALA 1 -0.119 -0.056 -0.408 1.00 0.00 ATOM 11 CB ALA 1 2.581 -1.760 1.132 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 5 ATOM 1 CL ALA 1 -0.711 0.249 2.300 1.00 0.00 ATOM 5 CLP ALA 1 -0.413 0.294 0.582 1.00 0.00 ATOM 6 OL ALA 1 -1.302 -0.345 0.923 1.00 0.00 ATOM 7 NL ALA 1 0.188 1.190 1.357 1.00 0.00 ATOM 9 CA ALA 1 -1.868 -1.268 -0.859 1.00 0.00 ATOM 10 HA ALA 1 1.257 2.462 0.333 1.00 0.00 ATOM 11 CB ALA 1 1.625 2.739 0.834 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 6 ATOM 1 CL ALA 1 1.726 0.072 -1.340 1.00 0.00 ATOM 5 CLP ALA 1 0.276 -0.187 2.093 1.00 0.00 ATOM 6 OL ALA 1 3.453 -1.380 2.311 1.00 0.00 ATOM 7 NL ALA 1 -1.796 1.155 -3.895 1.00 0.00 ATOM 9 CA ALA 1 0.715 0.847 -1.481 1.00 0.00 ATOM 10 HA ALA 1 -0.400 -0.900 2.392 1.00 0.00 ATOM 11 CB ALA 1 -0.759 -0.660 -1.433 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 7 ATOM 1 CL ALA 1 -1.904 2.132 3.402 1.00 0.00 ATOM 5 CLP ALA 1 0.238 0.227 -0.248 1.00 0.00 ATOM 6 OL ALA 1 0.948 0.987 -0.660 1.00 0.00 ATOM 7 NL ALA 1 -0.202 -3.291 0.558 1.00 0.00 ATOM 9 CA ALA 1 2.159 2.005 0.466 1.00 0.00 ATOM 10 HA ALA 1 -3.673 -1.187 0.464 1.00 0.00 ATOM 11 CB ALA 1 -0.238 -3.986 1.242 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 8 ATOM 1 CL ALA 1 -1.048 -1.735 -1.810 1.00 0.00 ATOM 5 CLP ALA 1 -0.480 0.126 0.637 1.00 0.00 ATOM 6 OL ALA 1 0.335 -1.142 1.004 1.00 0.00 ATOM 7 NL ALA 1 -1.272 -2.873 -0.534 1.00 0.00 ATOM 9 CA ALA 1 -0.098 -1.921 -0.936 1.00 0.00 ATOM 10 HA ALA 1 -2.763 4.072 -0.378 1.00 0.00 ATOM 11 CB ALA 1 5.815 -0.531 -1.221 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 9 ATOM 1 CL ALA 1 1.327 -0.262 -0.135 1.00 0.00 ATOM 5 CLP ALA 1 -0.421 0.795 0.416 1.00 0.00 ATOM 6 OL ALA 1 0.047 4.514 -0.507 1.00 0.00 ATOM 7 NL ALA 1 -0.977 -0.954 -0.276 1.00 0.00 ATOM 9 CA ALA 1 0.032 0.517 -0.511 1.00 0.00 ATOM 10 HA ALA 1 -1.033 0.278 4.615 1.00 0.00 ATOM 11 CB ALA 1 0.369 -0.111 -4.743 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 10 ATOM 1 CL ALA 1 -2.702 2.328 1.472 1.00 0.00 ATOM 5 CLP ALA 1 -0.113 -0.145 -0.348 1.00 0.00 ATOM 6 OL ALA 1 0.243 -0.055 -0.482 1.00 0.00 ATOM 7 NL ALA 1 -0.020 -3.369 0.812 1.00 0.00 ATOM 9 CA ALA 1 -0.248 -3.994 -0.683 1.00 0.00 ATOM 10 HA ALA 1 3.984 -0.978 2.422 1.00 0.00 ATOM 11 CB ALA 1 -0.210 1.820 -2.823 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 11 ATOM 1 CL ALA 1 0.646 -0.484 0.296 1.00 0.00 ATOM 5 CLP ALA 1 -0.799 -0.121 0.669 1.00 0.00 ATOM 6 OL ALA 1 -3.672 -1.016 0.684 1.00 0.00 ATOM 7 NL ALA 1 -3.204 -4.545 -1.162 1.00 0.00 ATOM 9 CA ALA 1 3.590 4.075 -0.029 1.00 0.00 ATOM 10 HA ALA 1 2.417 0.259 -0.984 1.00 0.00 ATOM 11 CB ALA 1 0.226 2.476 0.388 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 12 ATOM 1 CL ALA 1 0.612 1.661 1.265 1.00 0.00 ATOM 5 CLP ALA 1 0.538 -0.800 0.244 1.00 0.00 ATOM 6 OL ALA 1 3.751 1.368 0.056 1.00 0.00 ATOM 7 NL ALA 1 2.113 -2.383 2.664 1.00 0.00 ATOM 9 CA ALA 1 -0.270 0.667 -1.234 1.00 0.00 ATOM 10 HA ALA 1 -0.438 1.707 -1.913 1.00 0.00 ATOM 11 CB ALA 1 1.537 0.596 0.459 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 13 ATOM 1 CL ALA 1 0.459 -1.151 -1.231 1.00 0.00 ATOM 5 CLP ALA 1 -1.419 0.928 1.754 1.00 0.00 ATOM 6 OL ALA 1 2.698 5.399 0.280 1.00 0.00 ATOM 7 NL ALA 1 -3.743 -1.222 1.248 1.00 0.00 ATOM 9 CA ALA 1 0.064 -1.751 -1.531 1.00 0.00 ATOM 10 HA ALA 1 1.332 -1.487 -3.337 1.00 0.00 ATOM 11 CB ALA 1 -1.465 -0.065 1.725 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 14 ATOM 1 CL ALA 1 -0.710 1.523 -2.621 1.00 0.00 ATOM 5 CLP ALA 1 -2.218 0.360 -1.057 1.00 0.00 ATOM 6 OL ALA 1 4.130 -4.466 -1.130 1.00 0.00 ATOM 7 NL ALA 1 -2.388 0.410 3.677 1.00 0.00 ATOM 9 CA ALA 1 1.337 1.513 0.681 1.00 0.00 ATOM 10 HA ALA 1 0.460 -0.500 0.990 1.00 0.00 ATOM 11 CB ALA 1 -0.278 0.358 -0.436 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 15 ATOM 1 CL ALA 1 2.079 -4.326 3.034 1.00 0.00 ATOM 5 CLP ALA 1 -1.544 -1.032 -2.235 1.00 0.00 ATOM 6 OL ALA 1 1.011 -0.017 -3.316 1.00 0.00 ATOM 7 NL ALA 1 -2.514 1.752 3.001 1.00 0.00 ATOM 9 CA ALA 1 0.623 0.727 0.319 1.00 0.00 ATOM 10 HA ALA 1 0.081 0.315 1.133 1.00 0.00 ATOM 11 CB ALA 1 0.873 1.193 -0.880 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 16 ATOM 1 CL ALA 1 1.204 -1.169 -2.073 1.00 0.00 ATOM 5 CLP ALA 1 0.526 -0.271 -3.076 1.00 0.00 ATOM 6 OL ALA 1 -1.570 1.371 -3.374 1.00 0.00 ATOM 7 NL ALA 1 3.218 -2.092 0.582 1.00 0.00 ATOM 9 CA ALA 1 0.279 0.626 0.683 1.00 0.00 ATOM 10 HA ALA 1 -0.382 -0.365 1.037 1.00 0.00 ATOM 11 CB ALA 1 -0.794 -0.685 -0.104 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 17 ATOM 1 CL ALA 1 -2.588 3.772 -1.766 1.00 0.00 ATOM 5 CLP ALA 1 0.629 -4.880 -0.045 1.00 0.00 ATOM 6 OL ALA 1 -0.515 1.538 -2.272 1.00 0.00 ATOM 7 NL ALA 1 -1.615 1.644 0.561 1.00 0.00 ATOM 9 CA ALA 1 0.061 1.867 -0.042 1.00 0.00 ATOM 10 HA ALA 1 -0.858 0.764 0.234 1.00 0.00 ATOM 11 CB ALA 1 1.190 1.124 -0.379 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 18 ATOM 1 CL ALA 1 1.246 1.900 -0.300 1.00 0.00 ATOM 5 CLP ALA 1 1.497 0.436 -0.270 1.00 0.00 ATOM 6 OL ALA 1 -0.518 -0.138 -0.536 1.00 0.00 ATOM 7 NL ALA 1 -1.439 0.089 0.463 1.00 0.00 ATOM 9 CA ALA 1 0.064 -0.900 0.389 1.00 0.00 ATOM 10 HA ALA 1 1.044 0.817 0.468 1.00 0.00 ATOM 11 CB ALA 1 -0.890 -1.326 -0.140 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 19 ATOM 1 CL ALA 1 -0.097 -0.545 -0.060 1.00 0.00 ATOM 5 CLP ALA 1 3.452 1.557 -0.298 1.00 0.00 ATOM 6 OL ALA 1 -0.460 -0.676 -0.927 1.00 0.00 ATOM 7 NL ALA 1 -3.285 -0.072 1.516 1.00 0.00 ATOM 9 CA ALA 1 -2.696 -0.908 0.285 1.00 0.00 ATOM 10 HA ALA 1 -0.631 2.775 0.437 1.00 0.00 ATOM 11 CB ALA 1 -1.478 -3.053 -0.203 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 20 ATOM 1 CL ALA 1 1.302 -0.705 0.617 1.00 0.00 ATOM 5 CLP ALA 1 1.120 -0.399 0.825 1.00 0.00 ATOM 6 OL ALA 1 -0.313 -0.118 -0.585 1.00 0.00 ATOM 7 NL ALA 1 -0.438 0.007 0.043 1.00 0.00 ATOM 9 CA ALA 1 -1.358 1.374 -1.508 1.00 0.00 ATOM 10 HA ALA 1 -2.922 -0.986 -1.760 1.00 0.00 ATOM 11 CB ALA 1 1.525 1.900 0.349 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 21 ATOM 1 CL ALA 1 -0.058 -0.193 0.478 1.00 0.00 ATOM 5 CLP ALA 1 -2.688 -1.824 -0.450 1.00 0.00 ATOM 6 OL ALA 1 0.136 0.071 -0.332 1.00 0.00 ATOM 7 NL ALA 1 1.072 0.075 -0.476 1.00 0.00 ATOM 9 CA ALA 1 0.463 0.600 -1.792 1.00 0.00 ATOM 10 HA ALA 1 3.189 5.040 -1.663 1.00 0.00 ATOM 11 CB ALA 1 -2.272 -3.739 0.109 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 22 ATOM 1 CL ALA 1 -1.097 1.475 -0.730 1.00 0.00 ATOM 5 CLP ALA 1 2.759 3.698 -1.243 1.00 0.00 ATOM 6 OL ALA 1 -0.534 -1.098 -1.952 1.00 0.00 ATOM 7 NL ALA 1 -0.945 -0.181 0.710 1.00 0.00 ATOM 9 CA ALA 1 0.296 -1.350 -2.011 1.00 0.00 ATOM 10 HA ALA 1 -0.178 -2.159 -2.170 1.00 0.00 ATOM 11 CB ALA 1 0.474 0.997 0.351 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 23 ATOM 1 CL ALA 1 0.702 -1.257 -0.713 1.00 0.00 ATOM 5 CLP ALA 1 2.232 -3.026 0.306 1.00 0.00 ATOM 6 OL ALA 1 -0.300 0.096 -0.009 1.00 0.00 ATOM 7 NL ALA 1 -1.041 0.620 0.179 1.00 0.00 ATOM 9 CA ALA 1 0.660 -0.749 -0.957 1.00 0.00 ATOM 10 HA ALA 1 1.014 -0.132 -0.942 1.00 0.00 ATOM 11 CB ALA 1 -0.136 -0.182 0.085 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 24 ATOM 1 CL ALA 1 -0.018 0.401 -0.587 1.00 0.00 ATOM 5 CLP ALA 1 -6.126 1.679 -0.083 1.00 0.00 ATOM 6 OL ALA 1 0.442 -0.235 -0.852 1.00 0.00 ATOM 7 NL ALA 1 2.022 -0.330 -0.654 1.00 0.00 ATOM 9 CA ALA 1 -1.282 -0.737 -0.468 1.00 0.00 ATOM 10 HA ALA 1 -1.392 -1.115 -0.561 1.00 0.00 ATOM 11 CB ALA 1 0.363 0.533 0.115 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 25 ATOM 1 CL ALA 1 -1.081 1.792 -1.980 1.00 0.00 ATOM 5 CLP ALA 1 -0.330 0.052 0.259 1.00 0.00 ATOM 6 OL ALA 1 0.158 -0.039 0.753 1.00 0.00 ATOM 7 NL ALA 1 0.011 -0.105 -0.078 1.00 0.00 ATOM 9 CA ALA 1 -0.162 0.598 0.226 1.00 0.00 ATOM 10 HA ALA 1 0.121 1.138 0.268 1.00 0.00 ATOM 11 CB ALA 1 -0.338 -0.686 -0.030 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 26 ATOM 1 CL ALA 1 0.324 -0.321 -0.284 1.00 0.00 ATOM 5 CLP ALA 1 0.153 5.183 -2.052 1.00 0.00 ATOM 6 OL ALA 1 -0.018 -0.393 0.869 1.00 0.00 ATOM 7 NL ALA 1 -0.254 -0.334 0.149 1.00 0.00 ATOM 9 CA ALA 1 0.526 1.647 0.256 1.00 0.00 ATOM 10 HA ALA 1 0.755 2.047 0.409 1.00 0.00 ATOM 11 CB ALA 1 -0.207 -0.470 -0.182 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 27 ATOM 1 CL ALA 1 -0.103 0.298 0.001 1.00 0.00 ATOM 5 CLP ALA 1 -0.045 -1.625 -7.287 1.00 0.00 ATOM 6 OL ALA 1 0.361 1.309 6.026 1.00 0.00 ATOM 7 NL ALA 1 -1.080 0.071 0.398 1.00 0.00 ATOM 9 CA ALA 1 -0.285 -0.205 -0.218 1.00 0.00 ATOM 10 HA ALA 1 -0.628 -0.811 -0.253 1.00 0.00 ATOM 11 CB ALA 1 0.230 0.421 0.109 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 28 ATOM 1 CL ALA 1 1.969 -0.043 0.536 1.00 0.00 ATOM 5 CLP ALA 1 -1.232 -2.207 1.317 1.00 0.00 ATOM 6 OL ALA 1 -1.080 -2.259 1.291 1.00 0.00 ATOM 7 NL ALA 1 -1.412 -3.723 1.462 1.00 0.00 ATOM 9 CA ALA 1 -3.526 -1.760 1.731 1.00 0.00 ATOM 10 HA ALA 1 -2.616 -0.024 1.428 1.00 0.00 ATOM 11 CB ALA 1 -3.813 0.920 1.593 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 29 ATOM 1 CL ALA 1 0.000 -1.205 2.379 1.00 0.00 ATOM 5 CLP ALA 1 0.227 -1.929 -2.261 1.00 0.00 ATOM 6 OL ALA 1 1.512 -2.642 -2.421 1.00 0.00 ATOM 7 NL ALA 1 -0.768 -1.617 -3.990 1.00 0.00 ATOM 9 CA ALA 1 -0.941 -1.403 -3.052 1.00 0.00 ATOM 10 HA ALA 1 0.998 -2.146 -0.735 1.00 0.00 ATOM 11 CB ALA 1 0.977 -2.093 -0.412 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= 0.000 MODEL 30 ATOM 1 CL ALA 1 0.000 0.599 1.809 1.00 0.00 ATOM 5 CLP ALA 1 0.693 0.714 -0.204 1.00 0.00 ATOM 6 OL ALA 1 2.379 1.216 -0.720 1.00 0.00 ATOM 7 NL ALA 1 -0.605 0.209 -2.193 1.00 0.00 ATOM 9 CA ALA 1 -0.575 0.421 1.843 1.00 0.00 ATOM 10 HA ALA 1 1.886 1.277 3.582 1.00 0.00 ATOM 11 CB ALA 1 2.003 1.415 5.585 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= -0.000 MODEL 31 ATOM 1 CL ALA 1 0.000 1.916 5.450 1.00 0.00 ATOM 5 CLP ALA 1 -0.288 0.933 1.399 1.00 0.00 ATOM 6 OL ALA 1 -0.367 -0.533 1.731 1.00 0.00 ATOM 7 NL ALA 1 -0.232 1.942 1.197 1.00 0.00 ATOM 9 CA ALA 1 -0.398 1.917 -1.813 1.00 0.00 ATOM 10 HA ALA 1 -0.460 -0.041 -0.565 1.00 0.00 ATOM 11 CB ALA 1 -0.560 -0.156 -2.248 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= -0.000 MODEL 32 ATOM 1 CL ALA 1 -5.190 -1.632 0.437 1.00 0.00 ATOM 5 CLP ALA 1 -2.253 0.390 -0.091 1.00 0.00 ATOM 6 OL ALA 1 -1.854 0.851 -0.287 1.00 0.00 ATOM 7 NL ALA 1 -2.506 1.319 -0.779 1.00 0.00 ATOM 9 CA ALA 1 -0.701 -0.252 0.766 1.00 0.00 ATOM 10 HA ALA 1 -0.704 -1.087 1.320 1.00 0.00 ATOM 11 CB ALA 1 0.351 -1.813 2.095 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL TITLE frame t= -0.000 MODEL 33 ATOM 1 CL ALA 1 0.000 2.439 -0.447 1.00 0.00 ATOM 5 CLP ALA 1 -1.411 1.074 -2.252 1.00 0.00 ATOM 6 OL ALA 1 -0.595 0.807 -2.393 1.00 0.00 ATOM 7 NL ALA 1 -2.072 0.394 -3.143 1.00 0.00 ATOM 9 CA ALA 1 -3.190 1.483 -2.138 1.00 0.00 ATOM 10 HA ALA 1 -1.632 2.132 -1.108 1.00 0.00 ATOM 11 CB ALA 1 -2.221 2.639 -0.654 1.00 0.00 ATOM 15 CRP ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 16 OR ALA 1 -0.000 0.000 -0.000 1.00 0.00 ATOM 17 NR ALA 1 0.000 -0.000 -0.000 1.00 0.00 ATOM 19 CR ALA 1 -0.000 -0.000 0.000 1.00 0.00 TER ENDMDL
This input performs optimal alignment at every step and reports the rmsd so you know if you are far or close from the average structure. It takes the average structure and eigenvectors in form of a pdb. Note that beta and occupancy values in the pdb are neglected and all the weights are placed to 1 (differently from the RMSD colvar for example)
References
More information about how this action can be used is available in the following articles: - L. Sutto, M. D’Abramo, F. L. Gervasio, Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin. Journal of Chemical Theory and Computation. 6, 3640–3646 (2010) - V. Spiwok, P. Lipovová, B. Králová, Metadynamics in Essential Coordinates: Free Energy Simulation of Conformational Changes. The Journal of Physical Chemistry B. 111, 3073–3076 (2007)
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| AVERAGE | compulsory | none | a file in pdb format containing the reference structure and the atoms involved in the CV |
| EIGENVECTORS | compulsory | none | a file in pdb format containing the reference structure and the atoms involved in the CV |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| SQUARED_ROOT | optional | false | This should be set if you want RMSD instead of mean squared displacement |