Project ID: plumID:20.016
Source: Urea/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# Restart simulation. This command will append results of new simulations to the same output files, e.g. COLVAR. # RESTARTLOADLoads a library, possibly defining new actions. More detailsFILE=PairOrientationalEntropy.cppfile to be loaded
# Define groups for the CV The LOAD action with label calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=centers.dat # The command: # INCLUDE FILE=centers.dat # ensures PLUMED loads the contents of the file called centers.dat # The contents of this file are shown below (click the red comment to hide them). The INCLUDE action with label centers.dat calculates somethingc1:file to be includedCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=3,6 The CENTER action with label c1 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc2:
Quantity Description c1.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=11,14 The CENTER action with label c2 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc3:
Quantity Description c2.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=19,22 The CENTER action with label c3 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc4:
Quantity Description c3.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=27,30 The CENTER action with label c4 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc5:
Quantity Description c4.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=35,38 The CENTER action with label c5 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc6:
Quantity Description c5.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=43,46 The CENTER action with label c6 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc7:
Quantity Description c6.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=51,54 The CENTER action with label c7 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc8:
Quantity Description c7.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=59,62 The CENTER action with label c8 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc9:
Quantity Description c8.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=67,70 The CENTER action with label c9 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc10:
Quantity Description c9.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=75,78 The CENTER action with label c10 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc11:
Quantity Description c10.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=83,86 The CENTER action with label c11 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc12:
Quantity Description c11.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=91,94 The CENTER action with label c12 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc13:
Quantity Description c12.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=99,102 The CENTER action with label c13 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc14:
Quantity Description c13.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=107,110 The CENTER action with label c14 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc15:
Quantity Description c14.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=115,118 The CENTER action with label c15 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc16:
Quantity Description c15.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=123,126 The CENTER action with label c16 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc17:
Quantity Description c16.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=131,134 The CENTER action with label c17 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc18:
Quantity Description c17.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=139,142 The CENTER action with label c18 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc19:
Quantity Description c18.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=147,150 The CENTER action with label c19 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc20:
Quantity Description c19.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=155,158 The CENTER action with label c20 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc21:
Quantity Description c20.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=163,166 The CENTER action with label c21 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc22:
Quantity Description c21.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=171,174 The CENTER action with label c22 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc23:
Quantity Description c22.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=179,182 The CENTER action with label c23 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc24:
Quantity Description c23.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=187,190 The CENTER action with label c24 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc25:
Quantity Description c24.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=195,198 The CENTER action with label c25 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc26:
Quantity Description c25.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=203,206 The CENTER action with label c26 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc27:
Quantity Description c26.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=211,214 The CENTER action with label c27 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc28:
Quantity Description c27.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=219,222 The CENTER action with label c28 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc29:
Quantity Description c28.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=227,230 The CENTER action with label c29 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc30:
Quantity Description c29.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=235,238 The CENTER action with label c30 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc31:
Quantity Description c30.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=243,246 The CENTER action with label c31 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc32:
Quantity Description c31.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=251,254 The CENTER action with label c32 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc33:
Quantity Description c32.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=259,262 The CENTER action with label c33 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc34:
Quantity Description c33.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=267,270 The CENTER action with label c34 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc35:
Quantity Description c34.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=275,278 The CENTER action with label c35 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc36:
Quantity Description c35.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=283,286 The CENTER action with label c36 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc37:
Quantity Description c36.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=291,294 The CENTER action with label c37 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc38:
Quantity Description c37.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=299,302 The CENTER action with label c38 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc39:
Quantity Description c38.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=307,310 The CENTER action with label c39 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc40:
Quantity Description c39.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=315,318 The CENTER action with label c40 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc41:
Quantity Description c40.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=323,326 The CENTER action with label c41 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc42:
Quantity Description c41.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=331,334 The CENTER action with label c42 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc43:
Quantity Description c42.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=339,342 The CENTER action with label c43 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc44:
Quantity Description c43.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=347,350 The CENTER action with label c44 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc45:
Quantity Description c44.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=355,358 The CENTER action with label c45 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc46:
Quantity Description c45.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=363,366 The CENTER action with label c46 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc47:
Quantity Description c46.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=371,374 The CENTER action with label c47 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc48:
Quantity Description c47.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=379,382 The CENTER action with label c48 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc49:
Quantity Description c48.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=387,390 The CENTER action with label c49 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc50:
Quantity Description c49.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=395,398 The CENTER action with label c50 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc51:
Quantity Description c50.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=403,406 The CENTER action with label c51 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc52:
Quantity Description c51.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=411,414 The CENTER action with label c52 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc53:
Quantity Description c52.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=419,422 The CENTER action with label c53 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc54:
Quantity Description c53.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=427,430 The CENTER action with label c54 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc55:
Quantity Description c54.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=435,438 The CENTER action with label c55 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc56:
Quantity Description c55.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=443,446 The CENTER action with label c56 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc57:
Quantity Description c56.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=451,454 The CENTER action with label c57 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc58:
Quantity Description c57.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=459,462 The CENTER action with label c58 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc59:
Quantity Description c58.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=467,470 The CENTER action with label c59 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc60:
Quantity Description c59.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=475,478 The CENTER action with label c60 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc61:
Quantity Description c60.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=483,486 The CENTER action with label c61 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc62:
Quantity Description c61.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=491,494 The CENTER action with label c62 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc63:
Quantity Description c62.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=499,502 The CENTER action with label c63 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc64:
Quantity Description c63.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=507,510 The CENTER action with label c64 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc65:
Quantity Description c64.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=515,518 The CENTER action with label c65 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc66:
Quantity Description c65.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=523,526 The CENTER action with label c66 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc67:
Quantity Description c66.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=531,534 The CENTER action with label c67 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc68:
Quantity Description c67.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=539,542 The CENTER action with label c68 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc69:
Quantity Description c68.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=547,550 The CENTER action with label c69 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc70:
Quantity Description c69.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=555,558 The CENTER action with label c70 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc71:
Quantity Description c70.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=563,566 The CENTER action with label c71 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc72:
Quantity Description c71.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=571,574 The CENTER action with label c72 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc73:
Quantity Description c72.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=579,582 The CENTER action with label c73 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc74:
Quantity Description c73.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=587,590 The CENTER action with label c74 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc75:
Quantity Description c74.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=595,598 The CENTER action with label c75 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc76:
Quantity Description c75.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=603,606 The CENTER action with label c76 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc77:
Quantity Description c76.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=611,614 The CENTER action with label c77 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc78:
Quantity Description c77.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=619,622 The CENTER action with label c78 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc79:
Quantity Description c78.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=627,630 The CENTER action with label c79 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc80:
Quantity Description c79.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=635,638 The CENTER action with label c80 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc81:
Quantity Description c80.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=643,646 The CENTER action with label c81 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc82:
Quantity Description c81.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=651,654 The CENTER action with label c82 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc83:
Quantity Description c82.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=659,662 The CENTER action with label c83 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc84:
Quantity Description c83.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=667,670 The CENTER action with label c84 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc85:
Quantity Description c84.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=675,678 The CENTER action with label c85 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc86:
Quantity Description c85.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=683,686 The CENTER action with label c86 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc87:
Quantity Description c86.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=691,694 The CENTER action with label c87 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc88:
Quantity Description c87.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=699,702 The CENTER action with label c88 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc89:
Quantity Description c88.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=707,710 The CENTER action with label c89 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc90:
Quantity Description c89.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=715,718 The CENTER action with label c90 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc91:
Quantity Description c90.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=723,726 The CENTER action with label c91 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc92:
Quantity Description c91.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=731,734 The CENTER action with label c92 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc93:
Quantity Description c92.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=739,742 The CENTER action with label c93 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc94:
Quantity Description c93.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=747,750 The CENTER action with label c94 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc95:
Quantity Description c94.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=755,758 The CENTER action with label c95 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc96:
Quantity Description c95.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=763,766 The CENTER action with label c96 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc97:
Quantity Description c96.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=771,774 The CENTER action with label c97 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc98:
Quantity Description c97.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=779,782 The CENTER action with label c98 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc99:
Quantity Description c98.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=787,790 The CENTER action with label c99 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc100:
Quantity Description c99.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=795,798 The CENTER action with label c100 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc101:
Quantity Description c100.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=803,806 The CENTER action with label c101 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc102:
Quantity Description c101.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=811,814 The CENTER action with label c102 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc103:
Quantity Description c102.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=819,822 The CENTER action with label c103 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc104:
Quantity Description c103.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=827,830 The CENTER action with label c104 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc105:
Quantity Description c104.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=835,838 The CENTER action with label c105 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc106:
Quantity Description c105.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=843,846 The CENTER action with label c106 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc107:
Quantity Description c106.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=851,854 The CENTER action with label c107 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forc108:
Quantity Description c107.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=859,862the group of atoms that you are calculating the Gyration Tensor for
The CENTER action with label c108 calculates the following quantities:Ncenter:
Quantity Description c108.value the position of the center of mass GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,c18,c19,c20,c21,c22,c23,c24,c25,c26,c27,c28,c29,c30,c31,c32,c33,c34,c35,c36,c37,c38,c39,c40,c41,c42,c43,c44,c45,c46,c47,c48,c49,c50,c51,c52,c53,c54,c55,c56,c57,c58,c59,c60,c61,c62,c63,c64,c65,c66,c67,c68,c69,c70,c71,c72,c73,c74,c75,c76,c77,c78,c79,c80,c81,c82,c83,c84,c85,c86,c87,c88,c89,c90,c91,c92,c93,c94,c95,c96,c97,c98,c99,c100,c101,c102,c103,c104,c105,c106,c107,c108 # --- End of included input --- The GROUP action with label Ncenter calculates somethingC:the numerical indexes for the set of atoms in the groupGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=1-864:8 The GROUP action with label C calculates somethingO:the numerical indexes for the set of atoms in the groupGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=2-864:8 The GROUP action with label O calculates somethingN1:the numerical indexes for the set of atoms in the groupGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=3-864:8 The GROUP action with label N1 calculates somethingN2:the numerical indexes for the set of atoms in the groupGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=6-864:8 # Define the CVthe numerical indexes for the set of atoms in the group
The GROUP action with label N2 calculates somethingPAIR_ORIENTATIONAL_ENTROPY... LABEL=s1 CENTER=C START=Ncenter END=O MAXR=0.6 SIGMA=0.05,0.25 ... PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More detailsPAIR_ORIENTATIONAL_ENTROPY... LABEL=s2 CENTER=C START=N1 END=N2 MAXR=0.6 SIGMA=0.05,0.125 UP_DOWN_SYMMETRY ... PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More details
# Construct a bias potential using metadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=s1,s2 # Label of the CVthe input for this action is the scalar output from one or more other actionsPACE=500 # Pace in the deposition of the gaussiansthe frequency for hill additionHEIGHT=18.705 # Height of the gaussians in energy units kJ/mol. This is 5 kT.the heights of the Gaussian hillsSIGMA=0.1,0.1 # Width of the gaussian in CV unitsthe widths of the Gaussian hillsFILE=HILLS # File where the information of the gaussians is printeda file in which the list of added hills is storedBIASFACTOR=200.0 # Bias factor in well tempered simulationsuse well tempered metadynamics and use this bias factorTEMP=450.0 # Temperature in Kelvin. Only needed for well tempered simulationsthe system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-14.0,-14.0 # The following three lines define a grid for the calculation of the bias potential. Use it **always**.the lower bounds for the gridGRID_MAX=0.,0the upper bounds for the gridGRID_BIN=600,600the number of bins for the gridCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
# Print value of the CV and bias to a file named COLVAR The METAD action with label metad calculates the following quantities:
Quantity Description metad.bias the instantaneous value of the bias potential metad.rbias the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct] metad.rct the reweighting factor c(t) Print quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities