Action: PATHMSD
| Module | colvar |
|---|---|
| Description | Usage |
| This Colvar calculates path collective variables. |   |
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 |
|---|---|---|
| sss | scalar | the position on the path |
| zzz | scalar | the distance from the path |
Further details and examples
This Colvar calculates path collective variables.
Path collective variables were introduced in the paper cited in the bibliography. This CV defines a a curvilinear path using a set of reference configurations. Variables that measure the instantaneous position, sss, of the system on this path and the distance from this path, zzz, are then computed. The following input illustrates the syntax that is used with this variable
Click on the labels of the actions for more information on what each action computes
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#SETTINGS INPUTFILES=regtest/basic/rt39/all.pdb p1The PATHMSD action with label p1 calculates the following quantities:: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=
Quantity Type Description p1.sss scalar the position on the path p1.zzz scalar the distance from the path regtest/basic/rt39/all.pdbClick here to see an extract from this file.LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=500.0 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=4 NEIGH_SIZEsize of the neighbor list=8 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p1.sss,p1.zzz STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=colvar×FILE: regtest/basic/rt39/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
The NEIGH_STRIDE=4 and NEIGH_SIZE=8 keywords here control the neighbor list parameter (optional but
recommended for performance) and states that the neighbor list will be calculated every 4
steps and consider only the closest 8 member to the actual md snapshots.
When running with periodic boundary conditions, the atoms should be in the proper periodic image. This is done automatically since PLUMED 2.5, by considering the ordered list of atoms and rebuilding molecules with a procedure that is equivalent to that done in WHOLEMOLECULES. Notice that rebuilding is local to this action. This is different from WHOLEMOLECULES which actually modifies the coordinates stored in PLUMED.
In case you want to recover the old behavior you should use the NOPBC flag. In that case you need to take care that atoms are in the correct periodic image.
The implementation of this collective variable and of PROPERTYMAP is shared, as well as most input options.
References
More information about how this action can be used is available in the following articles: - D. Branduardi, F. L. Gervasio, M. Parrinello, From A to B in free energy space. The Journal of Chemical Physics. 126 (2007)
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| LAMBDA | compulsory | none | the lambda parameter is needed for smoothing, is in the units of plumed |
| REFERENCE | compulsory | none | the pdb is needed to provide the various milestones |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| NEIGH_SIZE | optional | not used | size of the neighbor list |
| NEIGH_STRIDE | optional | not used | how often the neighbor list needs to be calculated in time units |
| EPSILON | optional | not used | the maximum distance between the close and the current structure, the positive value turn on the close structure method |
| LOG_CLOSE | optional | not used | value 1 enables logging regarding the close structure |
| DEBUG_CLOSE | optional | not used | value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower |