Project ID: plumID:20.021
Source: plumed_K50.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
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MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=./ref.pdb WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-661,661-500:-1,1300-1475,1475-662:-1 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-2067 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=755,755,755,755,755,755,755,755,758,758,758,758,758,758,758,758,758,758,758,758,758,758,758,758,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,764,764,764,764,764,764,764,764,764,764,764,764, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=717,808,830,832,1245,1247,1251,1288,278,808,811,813,817,827,830,832,836,1245,1247,1288,1298,1310,1359,1362,278,808,811,813,817,827,830,832,836,1245,1247,1288,1298,1301,1308,1310,1359,1362,278,830,832,836,1247,1288,1298,1359,1362,1365,1366,1367, ... COORDINATION
rpv-2067: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-2067 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=22.68 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-2070 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=808,808,808,808,808,808,808,808,808,808,808,808,808,808,808,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=755,758,760,863,876,878,1074,1080,1126,1128,1132,1135,1247,1251,1310,436,758,760,878,1074,1076,1080,1126,1128,1135,1145,1148,1150,1154,1247,1251,1308,1310,436,758,760,1074,1080,1126,1128,1132,1145,1148,1150,1154,1245,1247,1251,1298,1301,1306,1308,1310,274,436,758,760,887,890,892,896,1074,1076,1080,1128,1145,1154,1301,1306,1308,1310, ... COORDINATION
rpv-2070: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-2070 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=31.95 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-2087 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1090,1090,1090,1090,1093,1093,1093,1093,1093,1093,1093,1095,1095,1095,1095,1095,1095,1099,1099,1099,1099,1099,1099, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=429,497,501,1040,429,492,495,497,501,1164,1170,427,429,492,495,497,501,429,492,495,497,501,1170, ... COORDINATION
rpv-2087: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-2087 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=20.93 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-2096 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1242,1242,1242,1242,1242,1242,1242,1242,1242,1242,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=700,703,745,1148,1150,1197,1200,1201,1202,1288,703,745,755,758,760,813,1132,1145,1148,1150,1197,1200,1201,1202,1288,1298,703,745,755,758,760,764,808,811,813,1150,1202,1288,1298,745,755,808,811,813,1126,1128,1132,1135,1145,1148,1150,1197,1200,1201,1202, ... COORDINATION
rpv-2096: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-2096 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=44.55 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-2099 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1288,1288,1288,1288,1288,1288,1288,1288,1288,1288,1288,1288, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=700,703,711,755,758,760,764,1242,1245,1247,1337,1362, ... COORDINATION
rpv-2099: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-2099 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=.720 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-1048 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=141,141,141,141,144,144,144,146,146,146, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=194,197,198,199,197,198,199,197,198,199, ... COORDINATION
rpv-1048: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-1048 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=3.60 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-1049 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=160,160,160,160,160,160,160,163,163,163,163,163,163,165,165,165,165,165,169,169,169,169,169,169,169, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=208,211,213,777,780,781,782,211,213,777,780,781,782,774,777,780,781,782,211,213,774,777,780,781,782, ... COORDINATION
rpv-1049: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-1049 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=7.75 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-1055 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=250,250,250,250,250,250,250,250,250,250,250,253,253,253,253,253,253,253,253,253,253,253,253,253,255,255,255,255,255,255,255,255,255,255,259,259,259,259,259,259,259,259,259,259,259,259,259,259,259,259, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=208,211,217,299,302,316,827,830,832,836,896,208,217,310,316,827,830,836,887,890,896,906,909,912,299,310,316,887,890,896,906,909,912,915,208,211,217,316,827,830,832,836,887,890,892,896,906,909,912,915, ... COORDINATION
rpv-1055: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-1055 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=41.50 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-1067 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=427,427,427,427,427,427,427,427,427,427,427,429,429,429,429,429,429,429,429,429,429,429,429,429,433,433,433,433,433,433,433,433,433,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=492,495,501,1076,1095,1145,1148,1154,1304,1306,1308,492,495,501,1074,1076,1090,1093,1095,1099,1145,1148,1154,1306,383,386,392,1076,1154,1304,1306,1308,1310,383,386,388,392,811,813,817,892,896,1074,1076,1080,1145,1148,1154,1301,1302,1304,1306,1308,1310, ... COORDINATION
rpv-1067: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-1067 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=12.42 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-1047 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=131,131, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=179,182, ... COORDINATION
rpv-1047: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-1047 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=.42 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-1054 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=239,239,239,239,239,239,239,239,239,242,242,242,242,242,242,242, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=288,291,299,302,1431,1432,1433,1435,1437,291,302,1431,1432,1433,1435,1437, ... COORDINATION
rpv-1054: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-1054 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=3.84 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-1062 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=351,351,351,351,351,354,354,354,354,357,357,357,357,357,358,358,358, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=324,327,328,329,402,327,328,329,402,402,467,469,470,473,469,470,473, ... COORDINATION
rpv-1062: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-1062 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=5.27 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=pv-1065 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=402,402,402,402,402,402,402,402,402,402,402,402, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=351,354,357,446,458,461,464,467,469,470,473,482, ... COORDINATION
rpv-1065: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-1065 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50. ATthe position of the restraint=.60 stat: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=pv-2067,pv-2070,pv-2087,pv-2096,pv-2099,pv-1048,pv-1049,pv-1055,pv-1067,pv-1047,pv-1054,pv-1062,pv-1065 PARAMETERSthe parameters of the arguments in your function=22.68,31.95,20.93,44.55,0.72,3.60,7.75,41.50,12.42,0.42,3.84,5.27,0.60 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=stat.* FILEthe name of the file on which to output these quantities=STAT STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=pv-2067,pv-2070,pv-2087,pv-2096,pv-2099,pv-1048,pv-1049,pv-1055,pv-1067,pv-1047,pv-1054,pv-1062,pv-1065 FILEthe name of the file on which to output these quantities=COORDINATION STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rpv-2067.bias,rpv-2070.bias,rpv-2087.bias,rpv-2096.bias,rpv-2099.bias,rpv-1048.bias,rpv-1049.bias,rpv-1055.bias,rpv-1067.bias,rpv-1047.bias,rpv-1054.bias,rpv-1062.bias,rpv-1065.bias FILEthe name of the file on which to output these quantities=RESTRAINTS STRIDE the frequency with which the quantities of interest should be output=500