Project ID: plumID:20.026
Source: plumed.dat
Originally used with PLUMED version: 2.5
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
rmsd_aThe MULTI_RMSD action with label rmsd_a calculates the following quantities:| Quantity | Type | Description |
| rmsd_a | scalar | the sum of the multiple RMSD distances |
: MULTI_RMSDCalculate RMSD distances for different domains and combine them. This action is a shortcut. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=OBP_lis_final.pdb TYPE the manner in which RMSD alignment is performed=MULTI-OPTIMAL
# rmsd_a: MULTI_RMSD REFERENCE=OBP_lis_final.pdb TYPE=MULTI-OPTIMAL
rmsd_a_ref1The CONSTANT action with label rmsd_a_ref1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_ref1 | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.547924,0.629924,0.575924,0.709924,0.469924,0.443924,0.140924,0.163924,0.0549242,0.0249242,-0.114076,-0.129076,-0.219076,0.105924,0.0299242,0.232924,0.300924,0.283924,0.435924,0.501924,0.506924,0.452924,0.576924,0.547924,0.582924,0.551924,0.656924,0.734924,0.661924,0.726924,0.253924,0.197924,0.0199242,0.0589242,-0.126076,-0.204076,-0.347076,-0.384076,-0.414076,-0.201076,-0.262076,-0.161076,-0.135076,-0.201076,-0.154076,-0.226076,-0.188076,-0.159076,-0.242076,-0.359076,-0.316076,-0.505076,-0.559076,-0.506076,-0.426076,-0.568076,-0.661076,-0.529076,-0.476076,-0.566076,-0.473076,-0.334076,-0.297076,-0.505076,-0.564076,-0.672076,-0.272121,-0.290121,-0.282121,-0.356121,-0.338121,-0.278121,-0.322121,-0.362121,-0.203121,-0.159121,-0.199121,-0.142121,-0.151121,-0.0921212,-0.0391212,-0.0521212,-0.0901212,0.0428788,0.0498788,0.138879,0.275879,0.326879,0.0788788,-0.0231212,0.353879,0.456879,0.156879,0.111879,0.293879,0.350879,-0.00912121,0.0638788,-0.239121,-0.274121,-0.256121,-0.315121,-0.354121,-0.448121,-0.309121,-0.129121,-0.116121,-0.0201212,-0.0261212,0.116879,0.215879,0.349879,0.163879,0.157879,0.198879,-0.0931212,-0.115121,-0.0911212,-0.100121,0.00287879,-0.0331212,0.0328788,0.0248788,0.147879,0.142879,0.283879,0.383879,0.362879,0.297879,0.389879,0.289879,0.316879,0.568015,0.623015,0.424015,0.417015,0.328015,0.224015,0.394015,0.483015,0.389015,0.532015,0.583015,0.724015,0.484015,0.296015,0.216015,0.297015,0.360015,0.197015,0.212015,0.106015,0.125015,0.204015,0.00501515,-0.0179848,0.0380152,0.0260152,-0.0779848,-0.138985,-0.0599848,-0.126985,0.0560152,-0.0249848,-0.0359848,0.0490152,-0.0469848,0.0710152,0.0350152,0.109015,-0.0609848,-0.0849848,-0.190985,-0.0199848,0.0760152,-0.0539848,0.0520152,0.0300152,0.192015,-0.195985,-0.275985,-0.474985,-0.386985,-0.457985,-0.313985,-0.229985,-0.180985,-0.521985,-0.601985,-0.467985,-0.383985,-0.509985,-0.441985,-0.467985,-0.401985,-0.291985,-0.662985,-0.714985
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=850,851,852,853,854,855,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971
The WHOLEMOLECULES action with label calculates somethingrmsd_a_cpos1The POSITION action with label rmsd_a_cpos1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_cpos1.x | vector | the x-component of the atom position |
| rmsd_a_cpos1.y | vector | the y-component of the atom position |
| rmsd_a_cpos1.z | vector | the z-component of the atom position |
: POSITIONCalculate the components of the position of an atom or atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe atom numbers that you would like to use the positions of=850,851,852,853,854,855,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971
rmsd_a_pos1The CONCATENATE action with label rmsd_a_pos1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_pos1 | vector | the concatenated vector/matrix that was constructed from the input values |
: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=rmsd_a_cpos1.x,rmsd_a_cpos1.y,rmsd_a_cpos1.z
rmsd_a_rmsd1The RMSD action with label rmsd_a_rmsd1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_rmsd1 | scalar | a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input |
: RMSD_VECTORCalculate the RMSD distance between the instaneous configuration and multiple reference configurations More details SQUARED This should be set if you want mean squared displacement instead of RMSD ARGthe labels of two actions that you are calculating the RMSD between=rmsd_a_pos1,rmsd_a_ref1 ALIGN the weights to use when aligning to the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE the weights to use when calculating the displacement from the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_a_ref2The CONSTANT action with label rmsd_a_ref2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_ref2 | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.420301,0.384301,0.325301,0.195301,0.134301,0.0913011,0.0373011,0.398301,0.402301,0.650301,0.633301,0.672301,0.562301,0.431301,0.536301,0.809301,0.827301,0.148301,0.0723011,0.201301,0.214301,0.0933011,0.332301,0.113301,0.146301,0.0793011,0.306301,0.367301,0.337301,0.447301,0.414301,0.224301,0.233301,0.100301,0.0783011,-0.0206989,-0.140699,-0.102699,-0.192699,-0.0516989,-0.0446989,-0.0286989,-0.000698925,-0.0356989,-0.0656989,0.0553011,0.00730108,0.128301,-0.144699,-0.263699,-0.153699,-0.0986989,-0.106699,0.0143011,0.0893011,0.0633011,0.00830108,0.198301,0.243301,0.127301,0.0723011,0.265301,0.344301,0.223301,0.246301,-0.212699,-0.228699,-0.294699,-0.266699,-0.408699,-0.487699,-0.412699,-0.407699,-0.446699,-0.498699,-0.533699,-0.332699,-0.312699,-0.291699,-0.414699,-0.428699,-0.597699,-0.545699,-0.514699,-0.373699,-0.506699,-0.519699,-0.473699,-0.466699,-0.460699,-0.417699,-0.597699,-0.601699,0.641269,0.639269,0.603269,0.547269,0.659269,0.501269,0.598269,0.495269,0.506269,0.270269,0.277269,0.135269,0.0362688,0.0492688,0.0372688,0.0672688,-0.0297312,-1.32173,-1.37373,-1.20873,-1.22173,-1.27873,-1.31573,-1.28473,-1.07173,-0.995731,-0.807731,-0.884731,-0.687731,-0.717731,-0.861731,-0.612731,-0.501731,-0.659731,-0.744731,-0.596731,-0.689731,-0.794731,-0.754731,-0.465731,-0.456731,-0.362731,-0.378731,-0.219731,-0.147731,-0.138731,-0.132731,-0.00973118,-0.181731,-0.178731,0.647269,0.636269,0.556269,0.491269,0.389269,0.253269,0.196269,0.435269,0.528269,0.170269,0.0782688,0.352269,0.385269,0.220269,0.167269,0.457269,0.453269,0.404269,0.394269,0.320269,0.264269,0.152269,0.00426882,-0.109731,0.406269,0.370269,0.586269,0.575269,0.481269,0.413269,0.429269,0.676269,0.698269,0.692269,0.745269,0.563269,0.573269,0.450269,0.441269,0.323269,0.223269,0.284269,0.245269,-0.688871,-0.781871,-0.583871,-0.643871,-0.727871,-0.542871,-0.828871,-0.503871,-0.381871,0.028129,-0.069871,0.082129,0.041129,0.119129,-0.108871,0.086129,0.159129,0.672129,0.631129,0.594129,0.442129,0.368129,0.415129,0.217129,0.634129,0.564129,0.696129,0.677129,0.617129,0.515129,0.406129,0.545129,0.494129,0.558129,0.606129,0.502129,0.484129,0.379129,0.612129,0.575129,0.698129,0.494129,0.400129,0.529129,0.397129,0.304129,0.159129,0.341129,0.628129,0.599129,0.185129,0.267129,0.079129,0.147129,0.061129,0.067129,0.142129,-0.011871,0.021129,-0.022871,-0.045871,-0.100871,-0.167871,-0.110871,-0.203871,0.030129,-0.091871,0.120129,0.215129,0.078129,0.197129,0.269129,0.161129,0.292129,-0.00887097,-0.120871,-0.333871,-0.236871,-0.427871,-0.487871,-0.609871,-0.745871,-0.662871,-0.866871,-0.836871,-0.947871,-1.06987,-0.885871,-0.786871,-0.959871,-0.851871,-1.01487,-1.13087
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=1439,1440,1441,1442,1443,1444,1445,1446,1447,1470,1471,1472,1473,1474,1475,1476,1477,1606,1607,1608,1609,1610,1611,1612,1613,1614,1624,1625,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1728,1729,1730,1731,1732,1733,1734,1735,1736,1737,1738,1739,1740,1741,1742,1743,1744,1745,1746,1747,1748,1749,1750,1751,1752,1753,1780,1781,1782,1783,1784,1802,1803,1804,1805,1806,1807,1808,1809,1810,1811,1812,1813
rmsd_a_cpos2The POSITION action with label rmsd_a_cpos2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_cpos2.x | vector | the x-component of the atom position |
| rmsd_a_cpos2.y | vector | the y-component of the atom position |
| rmsd_a_cpos2.z | vector | the z-component of the atom position |
: POSITIONCalculate the components of the position of an atom or atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe atom numbers that you would like to use the positions of=1439,1440,1441,1442,1443,1444,1445,1446,1447,1470,1471,1472,1473,1474,1475,1476,1477,1606,1607,1608,1609,1610,1611,1612,1613,1614,1624,1625,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1728,1729,1730,1731,1732,1733,1734,1735,1736,1737,1738,1739,1740,1741,1742,1743,1744,1745,1746,1747,1748,1749,1750,1751,1752,1753,1780,1781,1782,1783,1784,1802,1803,1804,1805,1806,1807,1808,1809,1810,1811,1812,1813
rmsd_a_pos2The CONCATENATE action with label rmsd_a_pos2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_pos2 | vector | the concatenated vector/matrix that was constructed from the input values |
: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=rmsd_a_cpos2.x,rmsd_a_cpos2.y,rmsd_a_cpos2.z
rmsd_a_rmsd2The RMSD action with label rmsd_a_rmsd2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_rmsd2 | scalar | a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input |
: RMSD_VECTORCalculate the RMSD distance between the instaneous configuration and multiple reference configurations More details SQUARED This should be set if you want mean squared displacement instead of RMSD ARGthe labels of two actions that you are calculating the RMSD between=rmsd_a_pos2,rmsd_a_ref2 ALIGN the weights to use when aligning to the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE the weights to use when calculating the displacement from the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_a_ref3The CONSTANT action with label rmsd_a_ref3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_ref3 | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.315493,-0.321493,-0.252493,-0.190493,-0.0794929,0.00150714,0.00150714,-0.0514929,0.0795071,0.125507,0.0535071,-0.112493,-0.168493,0.101507,0.181507,-0.0694929,-0.121493,0.0395071,0.0295071,-0.343493,-0.289493,-0.335493,-0.316493,-0.222493,-0.0994929,0.0255071,0.0755071,0.0685071,0.0545071,0.0335071,0.159507,0.232507,0.136507,0.141507,0.191507,0.250507,-0.243493,-0.232493,-0.280493,-0.255493,-0.315493,-0.313493,-0.175493,-0.0734929,-0.101493,-0.147493,-0.212493,0.0575071,0.134507,-0.0214929,0.000507143,0.0815071,0.183507,-0.436493,-0.435493,-0.313493,-0.294493,-0.210493,-0.0824929,-0.0664929,-0.159493,0.0525071,0.121507,0.0705071,-0.272493,-0.259493,-0.336493,-0.329493,-0.385493,-0.431493,-0.519493,-0.311493,-0.599493,-0.490493,-0.476493,-0.347493,-0.340493,-0.274493,-0.153493,-0.0624929,-0.0684929,-0.349493,-0.299493,-0.0614929,-0.0684929,0.0535071,0.138507,0.145507,0.00750714,0.208507,0.151507,0.151507,-0.0554929,-0.0994929,-0.0704929,-0.167493,-0.306493,-0.377493,-0.343493,-0.369493,-0.297493,-0.509493,-0.572493,-0.500493,-0.559493,-0.567493,-0.651493,0.0535071,0.0365071,0.170507,0.178507,0.297507,0.415507,0.412507,0.439507,0.337507,0.383507,0.154507,0.162507,0.231507,0.312507,0.316507,0.399507,0.417507,0.480507,0.541507,0.656507,0.636507,0.535507,0.783507,0.805507,0.738507,0.716507,0.886507,0.968507,0.864507,0.945507,0.880507,0.406507,0.440507,-0.18865,-0.16465,-0.08465,0.02235,-0.02565,-0.13065,-0.20365,0.02635,-0.14265,-0.22965,-0.04765,0.12135,0.20235,-0.03065,-0.08565,0.13835,0.19435,0.06735,0.05135,-0.01865,0.00835,-0.06865,-0.13765,-0.00765,-0.02565,0.04635,0.01335,-0.09165,0.17135,0.19235,0.09935,0.05435,0.25735,0.35735,0.22235,0.29335,0.14235,0.20535,0.19935,0.15135,0.34135,0.39935,0.41635,0.50135,0.59135,0.32635,0.24035,0.48335,0.53135,0.31835,0.24935,0.39635,0.37735,0.39035,0.50635,0.36935,0.31535,0.47035,0.45735,0.55035,0.57835,0.60935,0.58935,0.67135,0.60835,0.65035,0.67735,0.65635,0.81235,0.88535,0.79235,0.93135,0.88235,0.83835,0.91535,0.76435,0.71735,0.89035,0.90835,1.01135,0.78135,1.02035,1.11235,-0.26565,-0.21565,-0.23565,-0.11665,0.00035,0.05835,0.12435,-0.34665,-0.38865,-0.56965,-0.53365,-0.50065,-0.38265,-0.40565,-0.51865,-0.59565,-0.30265,-0.23865,-0.52765,-0.60665,-0.31065,-0.23465,-0.42965,-0.46165,-0.46765,-0.49565,-0.43965,-0.43365,-0.41565,-0.40065,-0.28165,-0.52565,-0.52065,-0.48465,-0.55465,-0.49065,-0.51965,-0.63365,-0.63565,-0.69365,-0.65565,-0.81365,-0.86965,-0.78565,-0.66865,-0.63565,-0.81465,-0.90165,-0.57465,-0.48765,-0.72265,-0.71865,-0.60465,-0.49665,-0.42565,-0.93265,-0.98365,-0.599121,-0.696121,-0.516121,-0.605121,-0.698121,-0.683121,-0.602121,-0.824121,-0.789121,-0.803121,-0.878121,-0.906121,-0.859121,-1.00812,-1.05712,-1.03712,-1.11512,-1.08412,-1.19212,-0.412121,-0.304121,0.0188786,-0.0511214,0.0898786,0.000878571,0.0508786,0.175879,0.204879,-0.00412143,-0.108121,0.246879,0.313879,0.0688786,0.0268786,0.191879,0.250879,0.107879,0.212879,-0.00712143,-0.0911214,-0.0191214,-0.160121,-0.226121,-0.185121,-0.130121,-0.328121,-0.342121,-0.229121,-0.169121,-0.386121,-0.468121,-0.334121,-0.369121,0.0598786,0.0998786,0.440879,0.358879,0.466879,0.383879,0.263879,0.188879,0.253879,0.322879,0.176879,0.489879,0.603879,0.395879,0.297879,0.426879,0.299879,0.216879,0.216879,0.120879,0.535879,0.629879,0.906879,0.818879,0.928879,0.837879,0.903879,0.826879,0.958879,1.02288,0.740879,0.826879,0.653879,0.697879,0.600879,0.570879,0.664879,0.615879,0.499879,0.383879,0.465879,0.254879,0.263879,0.322879,0.285879,0.216879,0.390879,0.441879,0.328879,0.288879,0.436879,0.488879,0.408879,0.470879,0.170879,0.0528786,0.228879,0.327879,0.159879,0.255879,0.351879,0.340879,0.0558786,-0.0521214,-0.389121,-0.313121,-0.509121,-0.571121,-0.694121,-0.490121,-0.400121,-0.513121,-0.384121,-0.330121,-0.257121,-0.235121,-0.378121,-0.441121,-0.246121,-0.184121,-0.368121,-0.441121,-0.297121,-0.315121,-0.340121,-0.575121,-0.682121
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=3349,3350,3351,3352,3353,3354,3355,3356,3357,3358,3359,3360,3361,3362,3363,3364,3365,3366,3367,3368,3369,3385,3386,3387,3388,3389,3390,3391,3392,3393,3394,3395,3396,3397,3398,3399,3400,3401,3402,3403,3404,3405,3406,3407,3408,3409,3410,3411,3412,3413,3414,3415,3416,3417,3418,3437,3438,3439,3440,3441,3442,3443,3444,3445,3446,3447,3448,3449,3450,3451,3452,3453,3454,3455,3456,3475,3476,3477,3478,3479,3480,3481,3482,3603,3604,3605,3606,3607,3608,3609,3610,3611,3631,3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643,3644,3645,3646,3647,3648,3649,3650,3651,3652,3653,3654,3655,3686,3687,3688,3689,3690,3691,3692,3693,3694,3695,3696,3697,3698,3699,3700,3701,3702,3703,3704,3705,3706,3707,3708
rmsd_a_cpos3The POSITION action with label rmsd_a_cpos3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_cpos3.x | vector | the x-component of the atom position |
| rmsd_a_cpos3.y | vector | the y-component of the atom position |
| rmsd_a_cpos3.z | vector | the z-component of the atom position |
: POSITIONCalculate the components of the position of an atom or atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe atom numbers that you would like to use the positions of=3349,3350,3351,3352,3353,3354,3355,3356,3357,3358,3359,3360,3361,3362,3363,3364,3365,3366,3367,3368,3369,3385,3386,3387,3388,3389,3390,3391,3392,3393,3394,3395,3396,3397,3398,3399,3400,3401,3402,3403,3404,3405,3406,3407,3408,3409,3410,3411,3412,3413,3414,3415,3416,3417,3418,3437,3438,3439,3440,3441,3442,3443,3444,3445,3446,3447,3448,3449,3450,3451,3452,3453,3454,3455,3456,3475,3476,3477,3478,3479,3480,3481,3482,3603,3604,3605,3606,3607,3608,3609,3610,3611,3631,3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643,3644,3645,3646,3647,3648,3649,3650,3651,3652,3653,3654,3655,3686,3687,3688,3689,3690,3691,3692,3693,3694,3695,3696,3697,3698,3699,3700,3701,3702,3703,3704,3705,3706,3707,3708
rmsd_a_pos3The CONCATENATE action with label rmsd_a_pos3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_pos3 | vector | the concatenated vector/matrix that was constructed from the input values |
: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=rmsd_a_cpos3.x,rmsd_a_cpos3.y,rmsd_a_cpos3.z
rmsd_a_rmsd3The RMSD action with label rmsd_a_rmsd3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_rmsd3 | scalar | a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input |
: RMSD_VECTORCalculate the RMSD distance between the instaneous configuration and multiple reference configurations More details SQUARED This should be set if you want mean squared displacement instead of RMSD ARGthe labels of two actions that you are calculating the RMSD between=rmsd_a_pos3,rmsd_a_ref3 ALIGN the weights to use when aligning to the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE the weights to use when calculating the displacement from the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_a_2The COMBINE action with label rmsd_a_2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_a_2 | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=rmsd_a_rmsd1,rmsd_a_rmsd2,rmsd_a_rmsd3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
rmsd_aThe CUSTOM action with label rmsd_a calculates the following quantities:| Quantity | Type | Description |
| rmsd_a | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=rmsd_a_2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- rmsd_bThe MULTI_RMSD action with label rmsd_b calculates the following quantities:| Quantity | Type | Description |
| rmsd_b | scalar | the sum of the multiple RMSD distances |
: MULTI_RMSDCalculate RMSD distances for different domains and combine them. This action is a shortcut. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=OBP_lsd_final.pdb TYPE the manner in which RMSD alignment is performed=MULTI-OPTIMAL
# rmsd_b: MULTI_RMSD REFERENCE=OBP_lsd_final.pdb TYPE=MULTI-OPTIMAL
rmsd_b_ref1The CONSTANT action with label rmsd_b_ref1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_ref1 | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.519333,0.585333,0.569333,0.722333,0.521333,0.485333,0.223333,0.252333,0.0833333,0.0103333,-0.0316667,-0.0386667,-0.169667,0.0643333,-0.0196667,0.154333,0.225333,0.157333,0.255333,0.287333,0.408333,0.482333,0.196333,0.104333,0.448333,0.552333,0.232333,0.157333,0.358333,0.396333,0.212333,0.147333,0.174333,0.201333,0.0603333,0.0143333,-0.0756667,-0.165667,-0.0406667,-0.0566667,-0.0686667,-0.105667,-0.0776667,-0.219667,-0.279667,-0.401667,-0.336667,-0.187667,-0.277667,-0.159667,-0.116667,-0.293667,-0.348667,-0.368667,-0.282667,-0.406667,-0.465667,-0.411667,-0.344667,-0.515667,-0.540667,-0.426667,-0.368667,-0.595667,-0.488667,-0.574667,0.273576,0.296576,0.223576,0.220576,0.0905758,0.0685758,-0.0634242,-0.0214242,-0.0434242,0.0215758,-0.0794242,-0.0224242,-0.136424,0.0365758,0.00157576,0.131576,0.158576,0.210576,0.324576,0.410576,0.405576,0.332576,0.508576,0.511576,0.504576,0.494576,0.600576,0.665576,0.604576,0.684576,0.120576,0.112576,-0.221424,-0.205424,-0.312424,-0.370424,-0.493424,-0.489424,-0.602424,-0.255424,-0.301424,-0.139424,-0.0894242,-0.0724242,0.0435758,0.103576,-0.0284242,-0.0194242,-0.0154242,-0.381424,-0.379424,-0.440424,-0.504424,-0.414424,-0.412424,-0.367424,-0.433424,-0.235424,-0.194424,-0.158424,-0.0164242,0.0665758,0.0545758,-0.0324242,-0.149424,-0.180424,0.576545,0.648545,0.447545,0.459545,0.391545,0.275545,0.467545,0.554545,0.426545,0.545545,0.652545,0.794545,0.618545,0.297545,0.214545,0.273545,0.338545,0.149545,0.176545,0.0545455,-0.0144545,0.0155455,0.0175455,0.0755455,-0.103455,-0.133455,-0.0804545,-0.125455,-0.138455,-0.202455,0.0385455,-0.0654545,0.0345455,0.129545,0.0195455,0.153545,0.138545,0.0525455,0.189545,-0.0604545,-0.173455,-0.0154545,0.0665455,-0.0784545,0.00254545,-0.0674545,0.124545,-0.218455,-0.302455,-0.420455,-0.329455,-0.423455,-0.295455,-0.186455,-0.136455,-0.496455,-0.582455,-0.482455,-0.420455,-0.552455,-0.500455,-0.525455,-0.445455,-0.358455,-0.702455,-0.784455
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=850,851,852,853,854,855,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971
rmsd_b_cpos1The POSITION action with label rmsd_b_cpos1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_cpos1.x | vector | the x-component of the atom position |
| rmsd_b_cpos1.y | vector | the y-component of the atom position |
| rmsd_b_cpos1.z | vector | the z-component of the atom position |
: POSITIONCalculate the components of the position of an atom or atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe atom numbers that you would like to use the positions of=850,851,852,853,854,855,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971
rmsd_b_pos1The CONCATENATE action with label rmsd_b_pos1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_pos1 | vector | the concatenated vector/matrix that was constructed from the input values |
: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=rmsd_b_cpos1.x,rmsd_b_cpos1.y,rmsd_b_cpos1.z
rmsd_b_rmsd1The RMSD action with label rmsd_b_rmsd1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_rmsd1 | scalar | a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input |
: RMSD_VECTORCalculate the RMSD distance between the instaneous configuration and multiple reference configurations More details SQUARED This should be set if you want mean squared displacement instead of RMSD ARGthe labels of two actions that you are calculating the RMSD between=rmsd_b_pos1,rmsd_b_ref1 ALIGN the weights to use when aligning to the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE the weights to use when calculating the displacement from the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_b_ref2The CONSTANT action with label rmsd_b_ref2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_ref2 | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.054828,0.056828,-0.010172,-0.054172,-0.151172,-0.128172,-0.190172,0.070828,0.015828,0.325828,0.322828,0.416828,0.414828,0.300828,0.407828,0.549828,0.565828,0.779828,0.707828,0.758828,0.611828,0.547828,0.593828,0.396828,0.803828,0.727828,0.794828,0.799828,0.713828,0.775828,0.949828,0.567828,0.530828,0.499828,0.536828,0.363828,0.335828,0.209828,0.440828,0.268828,0.270828,0.170828,0.175828,0.068828,0.044828,0.161828,0.160828,0.143828,-0.061172,-0.156172,-0.503172,-0.451172,-0.418172,-0.283172,-0.173172,-0.132172,-0.178172,-0.103172,-0.134172,-0.027172,-0.00217204,0.00482796,0.055828,0.042828,0.140828,-0.467172,-0.461172,-0.509172,-0.498172,-0.557172,-0.613172,-0.508172,-0.341172,-0.262172,-0.682172,-0.671172,-0.601172,-0.566172,-0.502172,-0.557172,-0.545172,-0.770172,-0.769172,-0.680172,-0.586172,-0.597172,-0.565172,-0.566172,-0.566172,-0.500172,-0.426172,-0.589172,-0.546172,0.664118,0.634118,0.573118,0.446118,0.480118,0.349118,0.366118,0.542118,0.536118,0.626118,0.578118,0.556118,0.404118,0.356118,0.342118,0.618118,0.624118,-0.914882,-0.910882,-0.834882,-0.833882,-0.972882,-0.757882,-0.967882,-0.688882,-0.614882,-0.421882,-0.511882,-0.323882,-0.304882,-0.251882,-0.368882,-0.452882,-0.301882,-0.219882,-0.340882,-0.347882,-0.428882,-0.428882,-0.245882,-0.122882,-0.309882,-0.408882,-0.237882,-0.309882,-0.309882,-0.445882,-0.189882,-0.229882,-0.303882,0.391118,0.443118,0.341118,0.322118,0.295118,0.400118,0.499118,0.176118,0.0891183,0.381118,0.454118,0.154118,0.0611183,0.261118,0.264118,0.209118,0.191118,0.119118,0.132118,-0.0118817,-0.0988817,-0.166882,-0.0918817,-0.184882,0.00211828,-0.0388817,0.268118,0.287118,0.194118,0.0801183,0.0801183,0.250118,0.310118,0.281118,0.395118,0.165118,0.173118,0.0571183,0.0541183,-0.0598817,-0.131882,-0.169882,-0.206882,-1.00871,-1.10371,-0.91271,-0.98671,-1.09971,-0.89471,-1.19471,-0.78671,-0.67671,-0.16871,-0.25671,-0.0767097,-0.0877097,0.00129032,-0.22771,-0.0327097,0.0892903,1.20429,1.27329,1.08329,1.03829,1.02929,0.90629,1.00729,1.09929,1.16229,0.86829,0.82529,0.79529,0.65629,0.63429,0.78829,0.70629,0.88029,0.92629,0.91829,1.06829,1.10029,1.14429,0.84529,0.84729,0.78229,0.76829,0.70429,0.57129,0.47329,0.40329,0.37929,0.78629,0.76029,0.0242903,0.0922903,-0.0847097,-0.0147097,-0.11771,-0.19971,-0.19271,-0.12271,-0.0657097,-0.28871,-0.36571,-0.20771,-0.23471,-0.28871,-0.33671,-0.14471,-0.26671,-0.0567097,0.0422903,-0.10071,0.0122903,0.10029,0.10829,0.23829,-0.18771,-0.30371,-0.51771,-0.42571,-0.59571,-0.68171,-0.80371,-0.96971,-0.88971,-1.08171,-1.04271,-1.13771,-1.25671,-1.06671,-0.96671,-1.12571,-1.01171,-1.18371,-1.29271
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=1439,1440,1441,1442,1443,1444,1445,1446,1447,1470,1471,1472,1473,1474,1475,1476,1477,1606,1607,1608,1609,1610,1611,1612,1613,1614,1624,1625,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1728,1729,1730,1731,1732,1733,1734,1735,1736,1737,1738,1739,1740,1741,1742,1743,1744,1745,1746,1747,1748,1749,1750,1751,1752,1753,1780,1781,1782,1783,1784,1802,1803,1804,1805,1806,1807,1808,1809,1810,1811,1812,1813
rmsd_b_cpos2The POSITION action with label rmsd_b_cpos2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_cpos2.x | vector | the x-component of the atom position |
| rmsd_b_cpos2.y | vector | the y-component of the atom position |
| rmsd_b_cpos2.z | vector | the z-component of the atom position |
: POSITIONCalculate the components of the position of an atom or atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe atom numbers that you would like to use the positions of=1439,1440,1441,1442,1443,1444,1445,1446,1447,1470,1471,1472,1473,1474,1475,1476,1477,1606,1607,1608,1609,1610,1611,1612,1613,1614,1624,1625,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1728,1729,1730,1731,1732,1733,1734,1735,1736,1737,1738,1739,1740,1741,1742,1743,1744,1745,1746,1747,1748,1749,1750,1751,1752,1753,1780,1781,1782,1783,1784,1802,1803,1804,1805,1806,1807,1808,1809,1810,1811,1812,1813
rmsd_b_pos2The CONCATENATE action with label rmsd_b_pos2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_pos2 | vector | the concatenated vector/matrix that was constructed from the input values |
: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=rmsd_b_cpos2.x,rmsd_b_cpos2.y,rmsd_b_cpos2.z
rmsd_b_rmsd2The RMSD action with label rmsd_b_rmsd2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_rmsd2 | scalar | a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input |
: RMSD_VECTORCalculate the RMSD distance between the instaneous configuration and multiple reference configurations More details SQUARED This should be set if you want mean squared displacement instead of RMSD ARGthe labels of two actions that you are calculating the RMSD between=rmsd_b_pos2,rmsd_b_ref2 ALIGN the weights to use when aligning to the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE the weights to use when calculating the displacement from the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_b_ref3The CONSTANT action with label rmsd_b_ref3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_ref3 | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.363479,-0.380479,-0.332479,-0.292479,-0.147479,-0.114479,-0.175479,-0.0384786,0.0135214,0.0625214,0.0655214,-0.0134786,-0.0834786,0.195521,0.281521,0.114521,0.122521,0.220521,0.321521,-0.441479,-0.417479,-0.348479,-0.325479,-0.234479,-0.155479,-0.0224786,-0.00947857,-0.0944786,0.0905214,0.0835214,0.116521,0.125521,0.216521,0.297521,0.227521,0.325521,-0.273479,-0.248479,-0.349479,-0.350479,-0.408479,-0.459479,-0.344479,-0.248479,-0.267479,-0.323479,-0.395479,-0.133479,-0.0504786,-0.210479,-0.194479,-0.110479,-0.0104786,-0.513479,-0.476479,-0.484479,-0.454479,-0.447479,-0.326479,-0.352479,-0.443479,-0.270479,-0.203479,-0.296479,-0.562479,-0.582479,-0.652479,-0.617479,-0.774479,-0.859479,-0.784479,-0.978479,-0.858479,-0.860479,-0.880479,-0.648479,-0.630479,-0.646479,-0.552479,-0.609479,-0.475479,-0.778479,-0.772479,0.139521,0.122521,0.225521,0.205521,0.0585214,0.0315214,0.0245214,0.371521,0.425521,0.349521,0.306521,0.293521,0.168521,0.0395214,-0.0404786,0.00752143,0.00352143,0.0525214,-0.152479,-0.199479,-0.108479,-0.136479,-0.187479,-0.281479,0.389521,0.373521,0.497521,0.504521,0.604521,0.708521,0.805521,0.648521,0.668521,0.684521,0.376521,0.409521,0.310521,0.366521,0.285521,0.495521,0.558521,0.560521,0.710521,0.794521,0.780521,0.731521,0.860521,0.833521,0.840521,0.814521,0.928521,1.00252,0.915521,1.00252,1.00052,0.536521,0.563521,-0.340286,-0.319286,-0.219286,-0.0972857,-0.0882857,-0.114286,-0.132286,-0.0292857,-0.0822857,-0.106286,-0.0332857,0.0167143,-0.00828571,-0.000285714,-0.0242857,0.0597143,0.117714,0.0527143,0.0857143,-0.174286,-0.0792857,-0.221286,-0.278286,-0.135286,-0.0992857,-0.0292857,0.107714,0.176714,-0.111286,-0.219286,0.161714,0.269714,-0.0592857,-0.127286,0.0787143,0.127714,0.00371429,0.0407143,0.0737143,0.0527143,0.198714,0.270714,0.325714,0.417714,0.488714,0.263714,0.188714,0.438714,0.487714,0.286714,0.217714,0.372714,0.367714,0.208714,0.253714,0.174714,0.180714,0.285714,0.366714,0.474714,0.556714,0.469714,0.397714,0.537714,0.372714,0.390714,0.401714,0.396714,0.480714,0.487714,0.541714,0.579714,0.505714,0.430714,0.494714,0.389714,0.378714,0.525714,0.611714,0.702714,0.704714,0.589714,0.654714,-0.0812857,-0.0562857,0.0167143,0.150714,0.189714,0.285714,0.275714,-0.0272857,0.00171429,-0.383286,-0.360286,-0.347286,-0.260286,-0.338286,-0.368286,-0.350286,-0.397286,-0.370286,-0.449286,-0.492286,-0.479286,-0.536286,-0.507286,-0.559286,-0.284286,-0.311286,-0.222286,-0.203286,-0.159286,-0.0962857,-0.0152857,-0.00728571,-0.255286,-0.227286,-0.508286,-0.467286,-0.415286,-0.400286,-0.405286,-0.429286,-0.460286,-0.408286,-0.394286,-0.365286,-0.247286,-0.166286,-0.472286,-0.575286,-0.233286,-0.144286,-0.455286,-0.530286,-0.336286,-0.308286,-0.209286,-0.517286,-0.494286,-0.6112,-0.7072,-0.5332,-0.6152,-0.6622,-0.7882,-0.8762,-0.5992,-0.8042,-0.8882,-0.6922,-0.4702,-0.3902,-0.6552,-0.7182,-0.4392,-0.3472,-0.5292,-0.5052,-0.4352,-0.3602,-0.0442,-0.1232,-0.0102,-0.1362,-0.1122,-0.0942,-0.0882,-0.1172,-0.1262,-0.0732,-0.0552,-0.0902,-0.0652,-0.0802,-0.0772,0.0418,0.1568,-0.0412,-0.1392,0.0078,-0.1182,-0.2042,-0.1642,-0.0842,-0.3262,-0.3602,-0.2392,-0.1882,-0.4032,-0.4872,-0.3602,-0.4012,0.1188,0.2268,0.5128,0.4168,0.6018,0.5558,0.4508,0.4578,0.3458,0.3298,0.2778,0.6538,0.7738,0.5618,0.4678,0.5838,0.4568,0.3348,0.4828,0.2058,0.6998,0.8028,1.0708,0.9728,1.1268,1.0418,0.9328,1.1368,1.1708,1.2748,0.7278,0.8228,0.6598,0.7298,0.7128,0.8288,0.5898,0.6458,0.5398,0.4058,0.4938,0.2748,0.2838,0.2578,0.3678,0.4638,0.1368,0.0438,0.3618,0.4508,0.1298,0.0418,0.2408,0.2218,0.1738,0.0548,0.2198,0.3178,0.1408,0.2328,0.1468,0.3418,0.0398,-0.0792,-0.1502,-0.0642,-0.2422,-0.3842,-0.4772,-0.3942,-0.3232,-0.5242,-0.4942,-0.6182,-0.6902,-0.6352,-0.6772,-0.6552,-0.8152,-0.8722,-0.7982,-0.8232,-0.8692,-0.9702,-0.9832,-0.6292,-0.7462
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=3349,3350,3351,3352,3353,3354,3355,3356,3357,3358,3359,3360,3361,3362,3363,3364,3365,3366,3367,3368,3369,3385,3386,3387,3388,3389,3390,3391,3392,3393,3394,3395,3396,3397,3398,3399,3400,3401,3402,3403,3404,3405,3406,3407,3408,3409,3410,3411,3412,3413,3414,3415,3416,3417,3418,3437,3438,3439,3440,3441,3442,3443,3444,3445,3446,3447,3448,3449,3450,3451,3452,3453,3454,3455,3456,3475,3476,3477,3478,3479,3480,3481,3482,3603,3604,3605,3606,3607,3608,3609,3610,3611,3631,3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643,3644,3645,3646,3647,3648,3649,3650,3651,3652,3653,3654,3655,3686,3687,3688,3689,3690,3691,3692,3693,3694,3695,3696,3697,3698,3699,3700,3701,3702,3703,3704,3705,3706,3707,3708
rmsd_b_cpos3The POSITION action with label rmsd_b_cpos3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_cpos3.x | vector | the x-component of the atom position |
| rmsd_b_cpos3.y | vector | the y-component of the atom position |
| rmsd_b_cpos3.z | vector | the z-component of the atom position |
: POSITIONCalculate the components of the position of an atom or atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe atom numbers that you would like to use the positions of=3349,3350,3351,3352,3353,3354,3355,3356,3357,3358,3359,3360,3361,3362,3363,3364,3365,3366,3367,3368,3369,3385,3386,3387,3388,3389,3390,3391,3392,3393,3394,3395,3396,3397,3398,3399,3400,3401,3402,3403,3404,3405,3406,3407,3408,3409,3410,3411,3412,3413,3414,3415,3416,3417,3418,3437,3438,3439,3440,3441,3442,3443,3444,3445,3446,3447,3448,3449,3450,3451,3452,3453,3454,3455,3456,3475,3476,3477,3478,3479,3480,3481,3482,3603,3604,3605,3606,3607,3608,3609,3610,3611,3631,3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643,3644,3645,3646,3647,3648,3649,3650,3651,3652,3653,3654,3655,3686,3687,3688,3689,3690,3691,3692,3693,3694,3695,3696,3697,3698,3699,3700,3701,3702,3703,3704,3705,3706,3707,3708
rmsd_b_pos3The CONCATENATE action with label rmsd_b_pos3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_pos3 | vector | the concatenated vector/matrix that was constructed from the input values |
: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=rmsd_b_cpos3.x,rmsd_b_cpos3.y,rmsd_b_cpos3.z
rmsd_b_rmsd3The RMSD action with label rmsd_b_rmsd3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_rmsd3 | scalar | a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input |
: RMSD_VECTORCalculate the RMSD distance between the instaneous configuration and multiple reference configurations More details SQUARED This should be set if you want mean squared displacement instead of RMSD ARGthe labels of two actions that you are calculating the RMSD between=rmsd_b_pos3,rmsd_b_ref3 ALIGN the weights to use when aligning to the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE the weights to use when calculating the displacement from the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_b_2The COMBINE action with label rmsd_b_2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_b_2 | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=rmsd_b_rmsd1,rmsd_b_rmsd2,rmsd_b_rmsd3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
rmsd_bThe CUSTOM action with label rmsd_b calculates the following quantities:| Quantity | Type | Description |
| rmsd_b | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=rmsd_b_2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=rmsd_a,rmsd_b ATthe position of the restraint=0.375,0.425 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100000.0,100000.0 LABELa label for the action so that its output can be referenced in the input to other actions=restraintThe RESTRAINT action with label restraint calculates the following quantities:| Quantity | Type | Description |
| restraint.bias | scalar | the instantaneous value of the bias potential |
| restraint.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=rmsd_a,rmsd_b ATthe position of the restraint=0.375,0.425 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100000.0,100000.0 LABELa label for the action so that its output can be referenced in the input to other actions=restraint SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0,0.0
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmsd_a,rmsd_b,restraint.bias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR
