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Action: REPARAMETERIZE_PATH

Module mapping
Description Usage
Take an input path with frames that are not equally spaced and make the frames equally spaced used in 0 tutorialsused in 0 eggs
This action outputs data to a file. You can read more about how PLUMED manages output files here

Details and examples

Take an input path with frames that are not equally spaced and make the frames equally spaced

This action is used by ADAPTIVE_PATH and pathtools. The algorithm in this action takes a set of trajectory frames along a PATH in input and adjusts them until they are all are equally spaced. To call this algorithm from pathtools you would use an input like this one:

plumed pathtoolsprint out a description of the keywords for an action in html This action has hidden defaults. More details --patha pdb file that contains an initial path in which the frames are not equally spaced in_path.pdb --metricthe measure to use to calculate the distance between frames EUCLIDEAN --outthe name of the file on which to output your path final_path.pdb

If you are using this action directly and not through pathtools or ADAPTIVE_PATH you will probably be using it in an input something like this if your path is defined using atomic coordinates:

Click on the labels of the actions for more information on what each action computes
tested on2.11
#SETTINGS INPUTFILES=regtest/trajectories/path_msd/all.pdb
rmsd: RMSDCalculate the RMSD with respect to a reference structure. This action is a shortcut and it has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/trajectories/path_msd/all.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/trajectories/path_msd/all.pdb
    
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
ATOM      8  HL  ALA     1      -1.798   0.982   0.124  1.00  1.00
ATOM      9  CA  ALA     1       0.026  -0.028   0.044  1.00  1.00
ATOM     10  HA  ALA     1       0.224  -1.060   0.284  1.00  1.00
ATOM     11  CB  ALA     1      -0.076   0.107  -1.483  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.776   0.577  1.00  1.00
ATOM     16  OR  ALA     1       1.900   1.463  -0.158  1.00  1.00
ATOM     17  NR  ALA     1       1.494   0.666   1.888  1.00  1.00
ATOM     18  HR  ALA     1       0.882   0.122   2.437  1.00  1.00
ATOM     19  CR  ALA     1       2.580   1.341   2.529  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.006   0.350   2.252  1.00  1.00
ATOM      5  CLP ALA     1      -1.680  -0.112   1.826  1.00  1.00
ATOM      6  OL  ALA     1      -1.025  -0.896   2.508  1.00  1.00
ATOM      7  NL  ALA     1      -1.220   0.368   0.654  1.00  1.00
ATOM      8  HL  ALA     1      -1.771   1.013   0.137  1.00  1.00
ATOM      9  CA  ALA     1       0.040  -0.029   0.062  1.00  1.00
ATOM     10  HA  ALA     1       0.210  -1.076   0.277  1.00  1.00
ATOM     11  CB  ALA     1      -0.066   0.148  -1.465  1.00  1.00
ATOM     15  CRP ALA     1       1.241   0.738   0.605  1.00  1.00
ATOM     16  OR  ALA     1       1.986   1.347  -0.125  1.00  1.00
ATOM     17  NR  ALA     1       1.446   0.694   1.940  1.00  1.00
ATOM     18  HR  ALA     1       0.796   0.210   2.481  1.00  1.00
ATOM     19  CR  ALA     1       2.544   1.350   2.582  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.002   0.343   2.271  1.00  1.00
ATOM      5  CLP ALA     1      -1.672  -0.125   1.828  1.00  1.00
ATOM      6  OL  ALA     1      -1.028  -0.942   2.486  1.00  1.00
ATOM      7  NL  ALA     1      -1.213   0.373   0.670  1.00  1.00
ATOM      8  HL  ALA     1      -1.752   1.033   0.169  1.00  1.00
ATOM      9  CA  ALA     1       0.041  -0.032   0.055  1.00  1.00
ATOM     10  HA  ALA     1       0.201  -1.079   0.245  1.00  1.00
ATOM     11  CB  ALA     1      -0.079   0.194  -1.466  1.00  1.00
ATOM     15  CRP ALA     1       1.257   0.720   0.601  1.00  1.00
ATOM     16  OR  ALA     1       2.057   1.240  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.422   0.730   1.942  1.00  1.00
ATOM     18  HR  ALA     1       0.740   0.303   2.500  1.00  1.00
ATOM     19  CR  ALA     1       2.528   1.373   2.598  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.144   1.457   1.417  1.00  1.00
ATOM      5  CLP ALA     1      -1.943   0.587   1.450  1.00  1.00
ATOM      6  OL  ALA     1      -1.588   0.028   2.480  1.00  1.00
ATOM      7  NL  ALA     1      -1.281   0.449   0.306  1.00  1.00
ATOM      8  HL  ALA     1      -1.578   0.914  -0.520  1.00  1.00
ATOM      9  CA  ALA     1      -0.132  -0.428   0.139  1.00  1.00
ATOM     10  HA  ALA     1      -0.264  -1.291   0.758  1.00  1.00
ATOM     11  CB  ALA     1      -0.066  -0.855  -1.329  1.00  1.00
ATOM     15  CRP ALA     1       1.193   0.220   0.554  1.00  1.00
ATOM     16  OR  ALA     1       2.195   0.098  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.224   0.872   1.737  1.00  1.00
ATOM     18  HR  ALA     1       0.399   0.943   2.273  1.00  1.00
ATOM     19  CR  ALA     1       2.413   1.511   2.254  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.140   1.441   1.453  1.00  1.00
ATOM      5  CLP ALA     1      -1.944   0.576   1.465  1.00  1.00
ATOM      6  OL  ALA     1      -1.587  -0.018   2.487  1.00  1.00
ATOM      7  NL  ALA     1      -1.274   0.465   0.322  1.00  1.00
ATOM      8  HL  ALA     1      -1.571   0.957  -0.486  1.00  1.00
ATOM      9  CA  ALA     1      -0.124  -0.418   0.135  1.00  1.00
ATOM     10  HA  ALA     1      -0.274  -1.304   0.729  1.00  1.00
ATOM     11  CB  ALA     1      -0.063  -0.813  -1.347  1.00  1.00
ATOM     15  CRP ALA     1       1.201   0.199   0.572  1.00  1.00
ATOM     16  OR  ALA     1       2.227   0.007  -0.072  1.00  1.00
ATOM     17  NR  ALA     1       1.215   0.910   1.709  1.00  1.00
ATOM     18  HR  ALA     1       0.369   1.020   2.200  1.00  1.00
ATOM     19  CR  ALA     1       2.393   1.536   2.237  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.140   1.420   1.442  1.00  1.00
ATOM      5  CLP ALA     1      -1.948   0.546   1.448  1.00  1.00
ATOM      6  OL  ALA     1      -1.618  -0.065   2.460  1.00  1.00
ATOM      7  NL  ALA     1      -1.255   0.469   0.311  1.00  1.00
ATOM      8  HL  ALA     1      -1.538   0.979  -0.490  1.00  1.00
ATOM      9  CA  ALA     1      -0.107  -0.412   0.124  1.00  1.00
ATOM     10  HA  ALA     1      -0.257  -1.312   0.685  1.00  1.00
ATOM     11  CB  ALA     1      -0.028  -0.770  -1.375  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.186   0.600  1.00  1.00
ATOM     16  OR  ALA     1       2.269  -0.069   0.026  1.00  1.00
ATOM     17  NR  ALA     1       1.193   0.966   1.687  1.00  1.00
ATOM     18  HR  ALA     1       0.333   1.114   2.120  1.00  1.00
ATOM     19  CR  ALA     1       2.377   1.589   2.240  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.110   1.698   0.880  1.00  1.00
ATOM      5  CLP ALA     1      -2.021   0.734   1.142  1.00  1.00
ATOM      6  OL  ALA     1      -1.859   0.257   2.258  1.00  1.00
ATOM      7  NL  ALA     1      -1.229   0.414   0.114  1.00  1.00
ATOM      8  HL  ALA     1      -1.371   0.826  -0.771  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.593   0.188  1.00  1.00
ATOM     10  HA  ALA     1      -0.481  -1.374   0.851  1.00  1.00
ATOM     11  CB  ALA     1       0.011  -1.180  -1.220  1.00  1.00
ATOM     15  CRP ALA     1       1.163  -0.060   0.716  1.00  1.00
ATOM     16  OR  ALA     1       2.227  -0.564   0.393  1.00  1.00
ATOM     17  NR  ALA     1       1.127   0.960   1.594  1.00  1.00
ATOM     18  HR  ALA     1       0.234   1.295   1.847  1.00  1.00
ATOM     19  CR  ALA     1       2.303   1.549   2.172  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.139   1.652   0.924  1.00  1.00
ATOM      5  CLP ALA     1      -2.039   0.698   1.169  1.00  1.00
ATOM      6  OL  ALA     1      -1.868   0.201   2.278  1.00  1.00
ATOM      7  NL  ALA     1      -1.239   0.411   0.139  1.00  1.00
ATOM      8  HL  ALA     1      -1.385   0.842  -0.737  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.574   0.193  1.00  1.00
ATOM     10  HA  ALA     1      -0.477  -1.381   0.833  1.00  1.00
ATOM     11  CB  ALA     1       0.029  -1.142  -1.231  1.00  1.00
ATOM     15  CRP ALA     1       1.162  -0.048   0.731  1.00  1.00
ATOM     16  OR  ALA     1       2.220  -0.597   0.472  1.00  1.00
ATOM     17  NR  ALA     1       1.122   1.024   1.537  1.00  1.00
ATOM     18  HR  ALA     1       0.233   1.395   1.752  1.00  1.00
ATOM     19  CR  ALA     1       2.300   1.629   2.102  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.706   1.088   0.468  1.00  1.00
ATOM      5  CLP ALA     1      -2.458   0.598   1.082  1.00  1.00
ATOM      6  OL  ALA     1      -2.390   0.404   2.277  1.00  1.00
ATOM      7  NL  ALA     1      -1.427   0.382   0.258  1.00  1.00
ATOM      8  HL  ALA     1      -1.513   0.559  -0.713  1.00  1.00
ATOM      9  CA  ALA     1      -0.157  -0.192   0.685  1.00  1.00
ATOM     10  HA  ALA     1      -0.343  -0.912   1.470  1.00  1.00
ATOM     11  CB  ALA     1       0.462  -0.936  -0.512  1.00  1.00
ATOM     15  CRP ALA     1       0.840   0.814   1.241  1.00  1.00
ATOM     16  OR  ALA     1       2.034   0.549   1.354  1.00  1.00
ATOM     17  NR  ALA     1       0.368   2.017   1.650  1.00  1.00
ATOM     18  HR  ALA     1      -0.613   2.169   1.589  1.00  1.00
ATOM     19  CR  ALA     1       1.215   3.044   2.195  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.699   1.173   0.487  1.00  1.00
ATOM      5  CLP ALA     1      -2.464   0.631   1.079  1.00  1.00
ATOM      6  OL  ALA     1      -2.402   0.386   2.275  1.00  1.00
ATOM      7  NL  ALA     1      -1.434   0.437   0.260  1.00  1.00
ATOM      8  HL  ALA     1      -1.516   0.652  -0.701  1.00  1.00
ATOM      9  CA  ALA     1      -0.174  -0.174   0.667  1.00  1.00
ATOM     10  HA  ALA     1      -0.377  -0.924   1.411  1.00  1.00
ATOM     11  CB  ALA     1       0.451  -0.859  -0.570  1.00  1.00
ATOM     15  CRP ALA     1       0.839   0.801   1.280  1.00  1.00
ATOM     16  OR  ALA     1       1.999   0.474   1.468  1.00  1.00
ATOM     17  NR  ALA     1       0.404   2.024   1.627  1.00  1.00
ATOM     18  HR  ALA     1      -0.565   2.225   1.505  1.00  1.00
ATOM     19  CR  ALA     1       1.262   3.025   2.214  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.653   0.990   1.121  1.00  1.00
ATOM      5  CLP ALA     1      -2.321   0.364   1.249  1.00  1.00
ATOM      6  OL  ALA     1      -2.006  -0.222   2.265  1.00  1.00
ATOM      7  NL  ALA     1      -1.498   0.501   0.205  1.00  1.00
ATOM      8  HL  ALA     1      -1.794   0.978  -0.603  1.00  1.00
ATOM      9  CA  ALA     1      -0.190  -0.127   0.128  1.00  1.00
ATOM     10  HA  ALA     1      -0.216  -1.086   0.627  1.00  1.00
ATOM     11  CB  ALA     1       0.159  -0.359  -1.359  1.00  1.00
ATOM     15  CRP ALA     1       0.933   0.668   0.793  1.00  1.00
ATOM     16  OR  ALA     1       2.107   0.313   0.705  1.00  1.00
ATOM     17  NR  ALA     1       0.604   1.770   1.498  1.00  1.00
ATOM     18  HR  ALA     1      -0.359   1.986   1.593  1.00  1.00
ATOM     19  CR  ALA     1       1.573   2.595   2.158  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.641   0.954   1.179  1.00  1.00
ATOM      5  CLP ALA     1      -2.294   0.335   1.290  1.00  1.00
ATOM      6  OL  ALA     1      -1.964  -0.273   2.288  1.00  1.00
ATOM      7  NL  ALA     1      -1.485   0.499   0.235  1.00  1.00
ATOM      8  HL  ALA     1      -1.803   0.995  -0.564  1.00  1.00
ATOM      9  CA  ALA     1      -0.175  -0.118   0.130  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.077   0.601  1.00  1.00
ATOM     11  CB  ALA     1       0.162  -0.300  -1.355  1.00  1.00
ATOM     15  CRP ALA     1       0.952   0.671   0.815  1.00  1.00
ATOM     16  OR  ALA     1       2.104   0.260   0.791  1.00  1.00
ATOM     17  NR  ALA     1       0.633   1.808   1.450  1.00  1.00
ATOM     18  HR  ALA     1      -0.328   2.065   1.503  1.00  1.00
ATOM     19  CR  ALA     1       1.608   2.627   2.129  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.635   0.925   1.244  1.00  1.00
ATOM      5  CLP ALA     1      -2.297   0.305   1.309  1.00  1.00
ATOM      6  OL  ALA     1      -1.941  -0.334   2.290  1.00  1.00
ATOM      7  NL  ALA     1      -1.500   0.490   0.251  1.00  1.00
ATOM      8  HL  ALA     1      -1.827   1.009  -0.537  1.00  1.00
ATOM      9  CA  ALA     1      -0.178  -0.110   0.119  1.00  1.00
ATOM     10  HA  ALA     1      -0.205  -1.094   0.536  1.00  1.00
ATOM     11  CB  ALA     1       0.147  -0.217  -1.379  1.00  1.00
ATOM     15  CRP ALA     1       0.943   0.643   0.832  1.00  1.00
ATOM     16  OR  ALA     1       2.074   0.198   0.871  1.00  1.00
ATOM     17  NR  ALA     1       0.637   1.821   1.423  1.00  1.00
ATOM     18  HR  ALA     1      -0.311   2.123   1.418  1.00  1.00
ATOM     19  CR  ALA     1       1.602   2.629   2.109  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.632   0.856   1.331  1.00  1.00
ATOM      5  CLP ALA     1      -2.282   0.250   1.355  1.00  1.00
ATOM      6  OL  ALA     1      -1.906  -0.403   2.301  1.00  1.00
ATOM      7  NL  ALA     1      -1.515   0.478   0.275  1.00  1.00
ATOM      8  HL  ALA     1      -1.860   0.990  -0.485  1.00  1.00
ATOM      9  CA  ALA     1      -0.192  -0.105   0.098  1.00  1.00
ATOM     10  HA  ALA     1      -0.204  -1.121   0.473  1.00  1.00
ATOM     11  CB  ALA     1       0.129  -0.136  -1.408  1.00  1.00
ATOM     15  CRP ALA     1       0.931   0.615   0.844  1.00  1.00
ATOM     16  OR  ALA     1       2.043   0.122   0.934  1.00  1.00
ATOM     17  NR  ALA     1       0.651   1.819   1.388  1.00  1.00
ATOM     18  HR  ALA     1      -0.283   2.155   1.349  1.00  1.00
ATOM     19  CR  ALA     1       1.624   2.595   2.115  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.628   0.823   1.358  1.00  1.00
ATOM      5  CLP ALA     1      -2.277   0.241   1.370  1.00  1.00
ATOM      6  OL  ALA     1      -1.871  -0.396   2.325  1.00  1.00
ATOM      7  NL  ALA     1      -1.525   0.469   0.284  1.00  1.00
ATOM      8  HL  ALA     1      -1.898   0.970  -0.482  1.00  1.00
ATOM      9  CA  ALA     1      -0.195  -0.094   0.086  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.122   0.423  1.00  1.00
ATOM     11  CB  ALA     1       0.146  -0.058  -1.413  1.00  1.00
ATOM     15  CRP ALA     1       0.919   0.599   0.874  1.00  1.00
ATOM     16  OR  ALA     1       1.997   0.065   1.039  1.00  1.00
ATOM     17  NR  ALA     1       0.655   1.830   1.373  1.00  1.00
ATOM     18  HR  ALA     1      -0.248   2.200   1.261  1.00  1.00
ATOM     19  CR  ALA     1       1.625   2.581   2.124  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.539   0.055   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -2.117  -0.208   1.378  1.00  1.00
ATOM      6  OL  ALA     1      -1.453  -0.902   2.125  1.00  1.00
ATOM      7  NL  ALA     1      -1.602   0.351   0.289  1.00  1.00
ATOM      8  HL  ALA     1      -2.185   0.875  -0.310  1.00  1.00
ATOM      9  CA  ALA     1      -0.243   0.129  -0.186  1.00  1.00
ATOM     10  HA  ALA     1      -0.041  -0.924  -0.159  1.00  1.00
ATOM     11  CB  ALA     1      -0.153   0.625  -1.651  1.00  1.00
ATOM     15  CRP ALA     1       0.852   0.806   0.637  1.00  1.00
ATOM     16  OR  ALA     1       2.007   0.400   0.594  1.00  1.00
ATOM     17  NR  ALA     1       0.508   1.855   1.401  1.00  1.00
ATOM     18  HR  ALA     1      -0.445   2.112   1.454  1.00  1.00
ATOM     19  CR  ALA     1       1.460   2.569   2.226  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.578   0.084   1.603  1.00  1.00
ATOM      5  CLP ALA     1      -2.140  -0.156   1.375  1.00  1.00
ATOM      6  OL  ALA     1      -1.473  -0.732   2.197  1.00  1.00
ATOM      7  NL  ALA     1      -1.623   0.335   0.237  1.00  1.00
ATOM      8  HL  ALA     1      -2.220   0.753  -0.416  1.00  1.00
ATOM      9  CA  ALA     1      -0.253   0.120  -0.195  1.00  1.00
ATOM     10  HA  ALA     1      -0.048  -0.931  -0.153  1.00  1.00
ATOM     11  CB  ALA     1      -0.128   0.612  -1.663  1.00  1.00
ATOM     15  CRP ALA     1       0.823   0.801   0.637  1.00  1.00
ATOM     16  OR  ALA     1       1.969   0.367   0.665  1.00  1.00
ATOM     17  NR  ALA     1       0.477   1.912   1.333  1.00  1.00
ATOM     18  HR  ALA     1      -0.468   2.199   1.317  1.00  1.00
ATOM     19  CR  ALA     1       1.410   2.627   2.163  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.113   1.661   1.504  1.00  1.00
ATOM      5  CLP ALA     1      -1.769   1.059   1.566  1.00  1.00
ATOM      6  OL  ALA     1      -1.201   0.940   2.629  1.00  1.00
ATOM      7  NL  ALA     1      -1.219   0.714   0.392  1.00  1.00
ATOM      8  HL  ALA     1      -1.742   0.797  -0.435  1.00  1.00
ATOM      9  CA  ALA     1       0.058   0.023   0.242  1.00  1.00
ATOM     10  HA  ALA     1      -0.001  -0.896   0.782  1.00  1.00
ATOM     11  CB  ALA     1       0.235  -0.295  -1.249  1.00  1.00
ATOM     15  CRP ALA     1       1.299   0.757   0.745  1.00  1.00
ATOM     16  OR  ALA     1       2.276   0.138   1.135  1.00  1.00
ATOM     17  NR  ALA     1       1.277   2.102   0.736  1.00  1.00
ATOM     18  HR  ALA     1       0.447   2.567   0.458  1.00  1.00
ATOM     19  CR  ALA     1       2.391   2.896   1.191  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
ATOM      9  CA  ALA     1       0.126   0.105   0.564  1.00  1.00
ATOM     10  HA  ALA     1       0.239  -0.555   1.391  1.00  1.00
ATOM     11  CB  ALA     1       0.215  -0.722  -0.739  1.00  1.00
ATOM     15  CRP ALA     1       1.311   1.068   0.623  1.00  1.00
ATOM     16  OR  ALA     1       2.369   0.726   1.149  1.00  1.00
ATOM     17  NR  ALA     1       1.156   2.292   0.077  1.00  1.00
ATOM     18  HR  ALA     1       0.273   2.549  -0.285  1.00  1.00
ATOM     19  CR  ALA     1       2.201   3.277   0.107  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.102   1.775   1.619  1.00  1.00
ATOM      5  CLP ALA     1      -1.661   1.466   1.659  1.00  1.00
ATOM      6  OL  ALA     1      -0.945   1.961   2.476  1.00  1.00
ATOM      7  NL  ALA     1      -1.205   0.663   0.688  1.00  1.00
ATOM      8  HL  ALA     1      -1.854   0.269   0.091  1.00  1.00
ATOM      9  CA  ALA     1       0.147   0.134   0.561  1.00  1.00
ATOM     10  HA  ALA     1       0.300  -0.545   1.355  1.00  1.00
ATOM     11  CB  ALA     1       0.237  -0.632  -0.776  1.00  1.00
ATOM     15  CRP ALA     1       1.306   1.133   0.628  1.00  1.00
ATOM     16  OR  ALA     1       2.361   0.819   1.176  1.00  1.00
ATOM     17  NR  ALA     1       1.129   2.345   0.068  1.00  1.00
ATOM     18  HR  ALA     1       0.252   2.577  -0.315  1.00  1.00
ATOM     19  CR  ALA     1       2.150   3.364   0.108  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.137   1.689   1.564  1.00  1.00
ATOM      5  CLP ALA     1      -1.674   1.466   1.595  1.00  1.00
ATOM      6  OL  ALA     1      -0.991   2.041   2.377  1.00  1.00
ATOM      7  NL  ALA     1      -1.178   0.640   0.664  1.00  1.00
ATOM      8  HL  ALA     1      -1.829   0.190   0.106  1.00  1.00
ATOM      9  CA  ALA     1       0.192   0.170   0.547  1.00  1.00
ATOM     10  HA  ALA     1       0.347  -0.550   1.313  1.00  1.00
ATOM     11  CB  ALA     1       0.333  -0.536  -0.821  1.00  1.00
ATOM     15  CRP ALA     1       1.325   1.194   0.686  1.00  1.00
ATOM     16  OR  ALA     1       2.348   0.906   1.293  1.00  1.00
ATOM     17  NR  ALA     1       1.165   2.398   0.103  1.00  1.00
ATOM     18  HR  ALA     1       0.311   2.617  -0.339  1.00  1.00
ATOM     19  CR  ALA     1       2.173   3.424   0.206  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.342   1.726   1.297  1.00  1.00
ATOM      5  CLP ALA     1      -1.882   1.644   1.449  1.00  1.00
ATOM      6  OL  ALA     1      -1.296   2.423   2.124  1.00  1.00
ATOM      7  NL  ALA     1      -1.259   0.684   0.740  1.00  1.00
ATOM      8  HL  ALA     1      -1.839   0.091   0.256  1.00  1.00
ATOM      9  CA  ALA     1       0.138   0.295   0.784  1.00  1.00
ATOM     10  HA  ALA     1       0.267  -0.321   1.638  1.00  1.00
ATOM     11  CB  ALA     1       0.437  -0.541  -0.481  1.00  1.00
ATOM     15  CRP ALA     1       1.207   1.385   0.899  1.00  1.00
ATOM     16  OR  ALA     1       2.160   1.248   1.674  1.00  1.00
ATOM     17  NR  ALA     1       1.092   2.478   0.129  1.00  1.00
ATOM     18  HR  ALA     1       0.291   2.586  -0.440  1.00  1.00
ATOM     19  CR  ALA     1       2.044   3.567   0.190  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.361   1.726   1.315  1.00  1.00
ATOM      5  CLP ALA     1      -1.890   1.687   1.423  1.00  1.00
ATOM      6  OL  ALA     1      -1.302   2.522   2.029  1.00  1.00
ATOM      7  NL  ALA     1      -1.285   0.691   0.757  1.00  1.00
ATOM      8  HL  ALA     1      -1.865   0.049   0.326  1.00  1.00
ATOM      9  CA  ALA     1       0.123   0.321   0.749  1.00  1.00
ATOM     10  HA  ALA     1       0.270  -0.331   1.585  1.00  1.00
ATOM     11  CB  ALA     1       0.408  -0.470  -0.534  1.00  1.00
ATOM     15  CRP ALA     1       1.192   1.410   0.900  1.00  1.00
ATOM     16  OR  ALA     1       2.114   1.273   1.701  1.00  1.00
ATOM     17  NR  ALA     1       1.111   2.493   0.112  1.00  1.00
ATOM     18  HR  ALA     1       0.326   2.609  -0.490  1.00  1.00
ATOM     19  CR  ALA     1       2.068   3.578   0.188  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.419   1.747   1.251  1.00  1.00
ATOM      5  CLP ALA     1      -1.947   1.630   1.371  1.00  1.00
ATOM      6  OL  ALA     1      -1.331   2.379   2.060  1.00  1.00
ATOM      7  NL  ALA     1      -1.380   0.668   0.616  1.00  1.00
ATOM      8  HL  ALA     1      -1.992   0.115   0.104  1.00  1.00
ATOM      9  CA  ALA     1       0.007   0.227   0.571  1.00  1.00
ATOM     10  HA  ALA     1       0.086  -0.578   1.262  1.00  1.00
ATOM     11  CB  ALA     1       0.288  -0.306  -0.835  1.00  1.00
ATOM     15  CRP ALA     1       1.132   1.190   0.974  1.00  1.00
ATOM     16  OR  ALA     1       1.974   0.858   1.808  1.00  1.00
ATOM     17  NR  ALA     1       1.199   2.390   0.352  1.00  1.00
ATOM     18  HR  ALA     1       0.482   2.643  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.218   3.363   0.657  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.430   1.748   1.261  1.00  1.00
ATOM      5  CLP ALA     1      -1.958   1.650   1.340  1.00  1.00
ATOM      6  OL  ALA     1      -1.333   2.471   1.961  1.00  1.00
ATOM      7  NL  ALA     1      -1.392   0.653   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -2.018   0.061   0.177  1.00  1.00
ATOM      9  CA  ALA     1      -0.005   0.219   0.569  1.00  1.00
ATOM     10  HA  ALA     1       0.083  -0.615   1.230  1.00  1.00
ATOM     11  CB  ALA     1       0.266  -0.275  -0.863  1.00  1.00
ATOM     15  CRP ALA     1       1.126   1.166   0.993  1.00  1.00
ATOM     16  OR  ALA     1       1.918   0.834   1.868  1.00  1.00
ATOM     17  NR  ALA     1       1.248   2.346   0.359  1.00  1.00
ATOM     18  HR  ALA     1       0.548   2.609  -0.299  1.00  1.00
ATOM     19  CR  ALA     1       2.271   3.308   0.675  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.438   1.702   1.306  1.00  1.00
ATOM      5  CLP ALA     1      -1.962   1.659   1.317  1.00  1.00
ATOM      6  OL  ALA     1      -1.332   2.532   1.870  1.00  1.00
ATOM      7  NL  ALA     1      -1.406   0.632   0.671  1.00  1.00
ATOM      8  HL  ALA     1      -2.029   0.002   0.252  1.00  1.00
ATOM      9  CA  ALA     1      -0.007   0.228   0.554  1.00  1.00
ATOM     10  HA  ALA     1       0.103  -0.631   1.184  1.00  1.00
ATOM     11  CB  ALA     1       0.255  -0.224  -0.899  1.00  1.00
ATOM     15  CRP ALA     1       1.124   1.169   1.002  1.00  1.00
ATOM     16  OR  ALA     1       1.889   0.829   1.901  1.00  1.00
ATOM     17  NR  ALA     1       1.265   2.342   0.365  1.00  1.00
ATOM     18  HR  ALA     1       0.590   2.614  -0.306  1.00  1.00
ATOM     19  CR  ALA     1       2.313   3.280   0.698  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.441   1.677   1.342  1.00  1.00
ATOM      5  CLP ALA     1      -1.971   1.666   1.304  1.00  1.00
ATOM      6  OL  ALA     1      -1.348   2.594   1.774  1.00  1.00
ATOM      7  NL  ALA     1      -1.408   0.602   0.696  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.062   0.329  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.235   0.538  1.00  1.00
ATOM     10  HA  ALA     1       0.114  -0.660   1.127  1.00  1.00
ATOM     11  CB  ALA     1       0.223  -0.161  -0.935  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.153   1.020  1.00  1.00
ATOM     16  OR  ALA     1       1.857   0.813   1.931  1.00  1.00
ATOM     17  NR  ALA     1       1.290   2.335   0.385  1.00  1.00
ATOM     18  HR  ALA     1       0.632   2.617  -0.298  1.00  1.00
ATOM     19  CR  ALA     1       2.337   3.252   0.749  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.443   1.670   1.352  1.00  1.00
ATOM      5  CLP ALA     1      -1.973   1.670   1.295  1.00  1.00
ATOM      6  OL  ALA     1      -1.351   2.609   1.744  1.00  1.00
ATOM      7  NL  ALA     1      -1.409   0.597   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.076   0.355  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.237   0.533  1.00  1.00
ATOM     10  HA  ALA     1       0.119  -0.663   1.113  1.00  1.00
ATOM     11  CB  ALA     1       0.217  -0.147  -0.945  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.152   1.023  1.00  1.00
ATOM     16  OR  ALA     1       1.849   0.808   1.938  1.00  1.00
ATOM     17  NR  ALA     1       1.296   2.334   0.388  1.00  1.00
ATOM     18  HR  ALA     1       0.638   2.620  -0.293  1.00  1.00
ATOM     19  CR  ALA     1       2.342   3.249   0.754  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.451   1.630   1.422  1.00  1.00
ATOM      5  CLP ALA     1      -1.983   1.689   1.248  1.00  1.00
ATOM      6  OL  ALA     1      -1.374   2.689   1.550  1.00  1.00
ATOM      7  NL  ALA     1      -1.421   0.569   0.756  1.00  1.00
ATOM      8  HL  ALA     1      -2.045  -0.151   0.513  1.00  1.00
ATOM      9  CA  ALA     1      -0.017   0.248   0.499  1.00  1.00
ATOM     10  HA  ALA     1       0.149  -0.681   1.023  1.00  1.00
ATOM     11  CB  ALA     1       0.171  -0.057  -0.999  1.00  1.00
ATOM     15  CRP ALA     1       1.111   1.147   1.033  1.00  1.00
ATOM     16  OR  ALA     1       1.807   0.781   1.969  1.00  1.00
ATOM     17  NR  ALA     1       1.327   2.329   0.410  1.00  1.00
ATOM     18  HR  ALA     1       0.679   2.635  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.372   3.237   0.799  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.331   1.449   1.617  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.399   1.408  1.00  1.00
ATOM      6  OL  ALA     1      -1.169   2.255   1.904  1.00  1.00
ATOM      7  NL  ALA     1      -1.424   0.371   0.676  1.00  1.00
ATOM      8  HL  ALA     1      -2.118  -0.203   0.289  1.00  1.00
ATOM      9  CA  ALA     1      -0.062   0.001   0.310  1.00  1.00
ATOM     10  HA  ALA     1      -0.008  -1.054   0.497  1.00  1.00
ATOM     11  CB  ALA     1       0.131   0.162  -1.216  1.00  1.00
ATOM     15  CRP ALA     1       1.142   0.546   1.099  1.00  1.00
ATOM     16  OR  ALA     1       1.741  -0.171   1.894  1.00  1.00
ATOM     17  NR  ALA     1       1.537   1.815   0.864  1.00  1.00
ATOM     18  HR  ALA     1       0.963   2.391   0.297  1.00  1.00
ATOM     19  CR  ALA     1       2.669   2.426   1.513  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.321   1.436   1.650  1.00  1.00
ATOM      5  CLP ALA     1      -1.870   1.422   1.372  1.00  1.00
ATOM      6  OL  ALA     1      -1.182   2.323   1.789  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.347   0.697  1.00  1.00
ATOM      8  HL  ALA     1      -2.106  -0.263   0.374  1.00  1.00
ATOM      9  CA  ALA     1      -0.057   0.008   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.002  -1.051   0.446  1.00  1.00
ATOM     11  CB  ALA     1       0.113   0.213  -1.212  1.00  1.00
ATOM     15  CRP ALA     1       1.139   0.538   1.102  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.196   1.881  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.803   0.879  1.00  1.00
ATOM     18  HR  ALA     1       0.972   2.397   0.326  1.00  1.00
ATOM     19  CR  ALA     1       2.672   2.407   1.539  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.318   1.434   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -1.871   1.426   1.363  1.00  1.00
ATOM      6  OL  ALA     1      -1.186   2.341   1.756  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.343   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.101  -0.279   0.398  1.00  1.00
ATOM      9  CA  ALA     1      -0.058   0.010   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.005  -1.051   0.433  1.00  1.00
ATOM     11  CB  ALA     1       0.109   0.227  -1.215  1.00  1.00
ATOM     15  CRP ALA     1       1.138   0.536   1.100  1.00  1.00
ATOM     16  OR  ALA     1       1.723  -0.202   1.878  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.802   0.887  1.00  1.00
ATOM     18  HR  ALA     1       0.970   2.398   0.335  1.00  1.00
ATOM     19  CR  ALA     1       2.675   2.402   1.547  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.297   1.417   1.700  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.437   1.310  1.00  1.00
ATOM      6  OL  ALA     1      -1.214   2.432   1.560  1.00  1.00
ATOM      7  NL  ALA     1      -1.412   0.320   0.746  1.00  1.00
ATOM      8  HL  ALA     1      -2.060  -0.372   0.544  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.025   0.282  1.00  1.00
ATOM     10  HA  ALA     1       0.023  -1.051   0.357  1.00  1.00
ATOM     11  CB  ALA     1       0.071   0.308  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.141   0.510   1.103  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.245   1.863  1.00  1.00
ATOM     17  NR  ALA     1       1.541   1.794   0.938  1.00  1.00
ATOM     18  HR  ALA     1       0.957   2.397   0.401  1.00  1.00
ATOM     19  CR  ALA     1       2.683   2.371   1.604  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.283   1.421   1.730  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.449   1.277  1.00  1.00
ATOM      6  OL  ALA     1      -1.222   2.476   1.436  1.00  1.00
ATOM      7  NL  ALA     1      -1.405   0.299   0.773  1.00  1.00
ATOM      8  HL  ALA     1      -2.034  -0.422   0.640  1.00  1.00
ATOM      9  CA  ALA     1      -0.063   0.028   0.272  1.00  1.00
ATOM     10  HA  ALA     1       0.015  -1.050   0.307  1.00  1.00
ATOM     11  CB  ALA     1       0.057   0.364  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.134   0.492   1.093  1.00  1.00
ATOM     16  OR  ALA     1       1.729  -0.288   1.825  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.779   0.976  1.00  1.00
ATOM     18  HR  ALA     1       0.945   2.388   0.456  1.00  1.00
ATOM     19  CR  ALA     1       2.682   2.335   1.653  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.265   1.435   1.760  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.457   1.257  1.00  1.00
ATOM      6  OL  ALA     1      -1.229   2.500   1.343  1.00  1.00
ATOM      7  NL  ALA     1      -1.398   0.292   0.802  1.00  1.00
ATOM      8  HL  ALA     1      -2.014  -0.454   0.728  1.00  1.00
ATOM      9  CA  ALA     1      -0.067   0.024   0.264  1.00  1.00
ATOM     10  HA  ALA     1       0.011  -1.049   0.257  1.00  1.00
ATOM     11  CB  ALA     1       0.028   0.426  -1.206  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.464   1.092  1.00  1.00
ATOM     16  OR  ALA     1       1.748  -0.346   1.781  1.00  1.00
ATOM     17  NR  ALA     1       1.532   1.754   1.029  1.00  1.00
ATOM     18  HR  ALA     1       0.931   2.385   0.536  1.00  1.00
ATOM     19  CR  ALA     1       2.676   2.280   1.721  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.236   1.453   1.772  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.473   1.217  1.00  1.00
ATOM      6  OL  ALA     1      -1.244   2.522   1.222  1.00  1.00
ATOM      7  NL  ALA     1      -1.388   0.292   0.824  1.00  1.00
ATOM      8  HL  ALA     1      -1.982  -0.485   0.827  1.00  1.00
ATOM      9  CA  ALA     1      -0.066   0.031   0.248  1.00  1.00
ATOM     10  HA  ALA     1       0.018  -1.048   0.230  1.00  1.00
ATOM     11  CB  ALA     1       0.011   0.464  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.452   1.088  1.00  1.00
ATOM     16  OR  ALA     1       1.767  -0.373   1.737  1.00  1.00
ATOM     17  NR  ALA     1       1.517   1.749   1.061  1.00  1.00
ATOM     18  HR  ALA     1       0.906   2.387   0.586  1.00  1.00
ATOM     19  CR  ALA     1       2.660   2.262   1.754  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.225   1.461   1.784  1.00  1.00
ATOM      5  CLP ALA     1      -1.878   1.466   1.191  1.00  1.00
ATOM      6  OL  ALA     1      -1.276   2.527   1.106  1.00  1.00
ATOM      7  NL  ALA     1      -1.375   0.274   0.839  1.00  1.00
ATOM      8  HL  ALA     1      -1.947  -0.517   0.921  1.00  1.00
ATOM      9  CA  ALA     1      -0.077   0.024   0.236  1.00  1.00
ATOM     10  HA  ALA     1       0.009  -1.048   0.194  1.00  1.00
ATOM     11  CB  ALA     1      -0.004   0.503  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.436   1.066  1.00  1.00
ATOM     16  OR  ALA     1       1.800  -0.403   1.678  1.00  1.00
ATOM     17  NR  ALA     1       1.483   1.736   1.091  1.00  1.00
ATOM     18  HR  ALA     1       0.861   2.388   0.647  1.00  1.00
ATOM     19  CR  ALA     1       2.642   2.246   1.792  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.212   1.465   1.797  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.470   1.168  1.00  1.00
ATOM      6  OL  ALA     1      -1.286   2.526   1.008  1.00  1.00
ATOM      7  NL  ALA     1      -1.363   0.265   0.860  1.00  1.00
ATOM      8  HL  ALA     1      -1.914  -0.534   1.016  1.00  1.00
ATOM      9  CA  ALA     1      -0.074   0.012   0.232  1.00  1.00
ATOM     10  HA  ALA     1       0.001  -1.058   0.173  1.00  1.00
ATOM     11  CB  ALA     1      -0.020   0.528  -1.210  1.00  1.00
ATOM     15  CRP ALA     1       1.147   0.408   1.060  1.00  1.00
ATOM     16  OR  ALA     1       1.827  -0.445   1.625  1.00  1.00
ATOM     17  NR  ALA     1       1.461   1.721   1.140  1.00  1.00
ATOM     18  HR  ALA     1       0.821   2.361   0.731  1.00  1.00
ATOM     19  CR  ALA     1       2.614   2.214   1.845  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.185   1.487   1.790  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.480   1.139  1.00  1.00
ATOM      6  OL  ALA     1      -1.293   2.532   0.896  1.00  1.00
ATOM      7  NL  ALA     1      -1.349   0.268   0.862  1.00  1.00
ATOM      8  HL  ALA     1      -1.881  -0.527   1.095  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.013   0.226  1.00  1.00
ATOM     10  HA  ALA     1      -0.006  -1.063   0.151  1.00  1.00
ATOM     11  CB  ALA     1      -0.019   0.539  -1.224  1.00  1.00
ATOM     15  CRP ALA     1       1.170   0.398   1.031  1.00  1.00
ATOM     16  OR  ALA     1       1.871  -0.463   1.540  1.00  1.00
ATOM     17  NR  ALA     1       1.447   1.706   1.159  1.00  1.00
ATOM     18  HR  ALA     1       0.788   2.362   0.800  1.00  1.00
ATOM     19  CR  ALA     1       2.602   2.205   1.868  1.00  1.00
END
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
ATOM      9  CA  ALA     1      -0.011  -0.077   0.099  1.00  1.00
ATOM     10  HA  ALA     1       0.155  -1.099   0.417  1.00  1.00
ATOM     11  CB  ALA     1       0.001  -0.097  -1.439  1.00  1.00
ATOM     15  CRP ALA     1       1.191   0.673   0.683  1.00  1.00
ATOM     16  OR  ALA     1       2.015   0.103   1.375  1.00  1.00
ATOM     17  NR  ALA     1       1.303   1.983   0.393  1.00  1.00
ATOM     18  HR  ALA     1       0.553   2.411  -0.109  1.00  1.00
ATOM     19  CR  ALA     1       2.395   2.811   0.843  1.00  1.00
END
FIXED

  
 DISPLACEMENT Calculate the vector of displacements instead of the length of this vector TYPE the manner in which RMSD alignment is performed=OPTIMAL
# Accumulate the average displacement between the reference path and the trajectories that have sampled the transition
disp: AVERAGE_PATH_DISPLACEMENTAccumulate the distances between the reference frames in the paths and the configurations visited This action has hidden defaults. More details ...
  ARGthe labels of the matrix that contains the vectors of displacements from each frame in the path=rmsd.disp STRIDE the frequency with which the average displacements should be collected and added to the average displacements=1
  METRICthe method to use for computing the displacement vectors between the reference frames={RMSD DISPLACEMENT TYPE=OPTIMAL ALIGN=1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE=1,1,1,1,1,1,1,1,1,1,1,1,1}
  METRIC_COMPONENTif the final action in your metric contains multiple components this keyword is used to specify the component that should be used=disp REFERENCElabels for actions that contain reference coordinates for each point on the path=rmsd_ref
...
# Now displace the original path by the accumulated displacement and reparameterize so that all frames are equally spaced
REPARAMETERIZE_PATHTake an input path with frames that are not equally spaced and make the frames equally spaced More details ...
  DISPLACE_FRAMESlabel of an action that tells us how to displace the frames=disp FIXED the frames in the path to fix=1,42
  METRICthe method to use for computing the displacement vectors between the reference frames={RMSD DISPLACEMENT TYPE=OPTIMAL ALIGN=1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE=1,1,1,1,1,1,1,1,1,1,1,1,1}
  METRIC_COMPONENTif the final action in your metric contains multiple components this keyword is used to specify the component that should be used=disp REFERENCElabels for actions that contain reference coordinates for each point on the path=rmsd_ref
  MAXCYLES number of cycles of the algorithm to run=100 TOL the tolerance to use for the path reparameterization algorithm=1E-4 STRIDE the frequency with which to reparameterize the path=0
...
# And output the final reparameterized path at the end of the simulation
DUMPPDBOutput PDB file. More details DESCRIPTIONthe title to use for your PDB output=PATH STRIDE the frequency with which the atoms should be output=0 FILEthe name of the file on which to output these quantities=outpatb.pdb ATOMSvalue containing positions of atoms that should be output=rmsd_ref ATOM_INDICESthe indices of the atoms in your PDB output=1-13

The method for reparameterizing paths that is implemented in this input is discussed in the example documentation for AVERAGE_PATH_DISPLACEMENT.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword Type Description
REFERENCE vector labels for actions that contain reference coordinates for each point on the path

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
REFERENCE input none labels for actions that contain reference coordinates for each point on the path
METRIC compulsory none the method to use for computing the displacement vectors between the reference frames
METRIC_COMPONENT compulsory none if the final action in your metric contains multiple components this keyword is used to specify the component that should be used
STRIDE compulsory 1 the frequency with which to reparameterize the path
FIXED compulsory 0 the frames in the path to fix
MAXCYLES compulsory 100 number of cycles of the algorithm to run
TOL compulsory 1E-4 the tolerance to use for the path reparameterization algorithm
DISPLACE_FRAMES optional not used label of an action that tells us how to displace the frames