Action: PROPERTYMAP
| Module | colvar |
|---|---|
| Description | Usage |
| Calculate generic property maps. |   |
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 |
|---|---|---|
| zzz | scalar | the minimum distance from the reference points |
| .#!custom | scalar | the names of the output components for this action depend on the actions input file see the example inputs below for details |
Further details and examples
Calculate generic property maps.
This colvar calculates the property maps according that is discussed in the paper by Spiwok in the bibligraphy below. The idea is to calculate properties like as X and Y as follows:
X=∑iXi∗exp(−λDi(x))∑iexp(−λDi(x))Y=∑iYi∗exp(−λDi(x))∑iexp(−λDi(x))⋯zzz=−1λlog(∑iexp(−λDi(x)))
The example input below shows how this works:
Click on the labels of the actions for more information on what each action computes
 |
#SETTINGS INPUTFILES=regtest/basic/rt40/allv.pdb p3The PROPERTYMAP action with label p3 calculates the following quantities:: PROPERTYMAPCalculate generic property maps. More details REFERENCEthe pdb is needed to provide the various milestones=
Quantity Type Description p3.X scalar the projection of the instanenous position in CV space on the coordinate X that is defined in the reference file p3.Y scalar the projection of the instanenous position in CV space on the coordinate Y that is defined in the reference file p3.zzz scalar the projection of the instanenous position in CV space on the coordinate zzz that is defined in the reference file regtest/basic/rt40/allv.pdbClick here to see an extract from this file.PROPERTYthe property to be used in the indexing: this goes in the REMARK field of the reference=X,Y LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=69087 NEIGH_SIZEsize of the neighbor list=8 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=4 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p3.X,p3.Y,p3.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 FMTthe format that should be used to output real numbers=%8.4f×FILE: regtest/basic/rt40/allv.pdb
REMARK X=1 Y=2 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 REMARK X=2 Y=3 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 REMARK X=3 Y=4 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 REMARK X=4 Y=5 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 REMARK X=5 Y=6 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 REMARK X=6 Y=7 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 REMARK X=7 Y=8 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 REMARK X=8 Y=9 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 REMARK X=9 Y=10 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 REMARK X=10 Y=11 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 REMARK X=11 Y=12 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 REMARK X=12 Y=13 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 REMARK X=13 Y=14 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 REMARK X=14 Y=15 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 REMARK X=15 Y=16 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 REMARK X=16 Y=17 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 REMARK X=17 Y=18 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 REMARK X=18 Y=19 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 REMARK X=19 Y=20 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 REMARK X=20 Y=21 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 REMARK X=21 Y=22 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 REMARK X=22 Y=23 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 REMARK X=23 Y=24 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 REMARK X=24 Y=25 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 REMARK X=25 Y=26 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 REMARK X=26 Y=27 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 REMARK X=27 Y=28 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 REMARK X=28 Y=29 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 REMARK X=29 Y=30 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 REMARK X=30 Y=31 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 REMARK X=31 Y=32 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 REMARK X=32 Y=33 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 REMARK X=33 Y=34 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 REMARK X=34 Y=35 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 REMARK X=35 Y=36 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 REMARK X=36 Y=37 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 REMARK X=37 Y=38 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 REMARK X=38 Y=39 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 REMARK X=39 Y=40 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 REMARK X=40 Y=41 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 REMARK X=41 Y=42 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 REMARK X=42 Y=43 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
In this case the input line instructs plumed to look for two properties X and Y with attached values in the REMARK
line of the reference pdb. The parameters Xi and Yi are provided in the input pdb and
Di(x) is the mean squared displacement after optimal alignment calculated on the pdb frames you input (see Kearsley).
The NEIGH_STRIDE=4 NEIGH_SIZE=8 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 using 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. If 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 PATHMSD is shared, as well as most input options.
References
More information about how this action can be used is available in the following articles: - V. Spiwok, B. Králová, Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap. The Journal of Chemical Physics. 135 (2011)
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 |
| PROPERTY | compulsory | none | the property to be used in the indexing: this goes in the REMARK field of the reference |
| 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 |