Project ID: plumID:23.045
Source: Path-CVs_MetaD/neca-bound/plumed.dat
Originally used with PLUMED version: 2.7.1
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
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=FApo.pdb
The MOLINFO action with label calculates somethingpThe PATHMSD action with label p calculates the following quantities:| Quantity | Type | Description |
| p.sss | scalar | the position on the path |
| p.zzz | scalar | the distance from the path |
: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=path_rmsd.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=122.00
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1458,3468
d2The DISTANCE action with label d2 calculates the following quantities:| Quantity | Type | Description |
| d2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3080,3468
H6The ALPHARMSD action with label H6 calculates the following quantities:| Quantity | Type | Description |
| H6 | scalar | if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix. If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix |
: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=220-252
H6: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=220-252 NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12 TYPE the manner in which RMSD alignment is performed=DRMSD
# H6: ALPHARMSD RESIDUES=220-252
H6_rmsdThe SECONDARY_STRUCTURE_RMSD action with label H6_rmsd calculates the following quantities:| Quantity | Type | Description |
| H6_rmsd | vector | a vector containing the rmsd distance between each of the residue segments and the reference structure |
: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=3386,3388,3390,3398,3399,3400,3402,3404,3417,3418,3419,3421,3423,3434,3435,3436,3438,3440,3456,3457,3458,3460,3462,3471,3472,3473,3475,3477,3487,3488,3489,3491,3493,3504,3505,3506,3508,3510,3514,3515,3516,3518,3520,3524,3525,3526,3528,3530,3546,3547,3548,3550,3552,3557,3558,3559,3561,3563,3576,3577,3578,3580,3582,3586,3587,3588,3590,3592,3605,3606,3607,3609,3611,3624,3625,3626,3628,3630,3640,3641,3642,3644,3645,3647,3648,3649,3651,3653,3666,3667,3668,3670,3672,3686,3687,3688,3690,3692,3696,3697,3698,3700,3702,3715,3716,3717,3719,3721,3726,3727,3728,3730,3732,3750,3751,3752,3754,3756,3769,3770,3771,3781,3778,3783,3784,3785,3787,3789,3802,3803,3804,3806,3808,3819,3820,3821,3823,3825,3838,3839,3840,3842,3844,3857,3858,3859,3861,3863,3871,3872,3873,3875,3877,3882,3883,3884,3886,3888,3902,3903,3904,3906,3908,3916,3917 TYPE the manner in which RMSD alignment is performed=DRMSD SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT2this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 SEGMENT3this is the lists of atoms in the segment that are being considered=10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT4this is the lists of atoms in the segment that are being considered=15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=0.733,0.519,5.298,1.763,0.81,4.301,3.166,0.543,4.881,1.527,-0.045,3.053,1.646,0.436,1.928,1.18,-1.312,3.254,0.924,-2.203,2.126,0.65,-3.626,2.626,-0.239,-1.711,1.261,-0.19,-1.815,0.032,-1.28,-1.172,1.891,-2.416,-0.661,1.127,-3.548,-0.217,2.056,-1.964,0.529,0.276,-2.364,0.659,-0.88,-1.13,1.391,0.856,-0.62,2.565,0.148,0.228,3.439,1.077,0.231,2.129,-1.032,0.179,2.733,-2.099,1.028,1.084,-0.833,1.872,0.593,-1.919,2.85,-0.462,-1.397,1.02,0.02,-3.049,1.317,0.227,-4.224,-0.051,-0.684,-2.696,-0.927,-1.261,-3.713,-1.933,-2.219,-3.074,-1.663,-0.171,-4.475,-1.916,-0.296,-5.673
H6_ltThe LESS_THAN action with label H6_lt calculates the following quantities:| Quantity | Type | Description |
| H6_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=H6_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
H6The SUM action with label H6 calculates the following quantities:| Quantity | Type | Description |
| H6 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=H6_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- H5The ALPHARMSD action with label H5 calculates the following quantities:| Quantity | Type | Description |
| H5 | scalar | if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix. If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix |
: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=198-209
H5: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=198-209 NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12 TYPE the manner in which RMSD alignment is performed=DRMSD
# H5: ALPHARMSD RESIDUES=198-209
H5_rmsdThe SECONDARY_STRUCTURE_RMSD action with label H5_rmsd calculates the following quantities:| Quantity | Type | Description |
| H5_rmsd | vector | a vector containing the rmsd distance between each of the residue segments and the reference structure |
: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=3026,3028,3030,3043,3044,3045,3047,3049,3053,3054,3055,3057,3059,3063,3064,3065,3067,3069,3087,3088,3089,3091,3093,3111,3112,3113,3115,3117,3128,3129,3130,3132,3134,3147,3148,3149,3151,3153,3169,3170,3171,3173,3175,3186,3187,3188,3190,3192,3203,3204,3205,3207,3209,3218,3219,3220,3222,3224,3229,3230 TYPE the manner in which RMSD alignment is performed=DRMSD SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT2this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 SEGMENT3this is the lists of atoms in the segment that are being considered=10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT4this is the lists of atoms in the segment that are being considered=15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=0.733,0.519,5.298,1.763,0.81,4.301,3.166,0.543,4.881,1.527,-0.045,3.053,1.646,0.436,1.928,1.18,-1.312,3.254,0.924,-2.203,2.126,0.65,-3.626,2.626,-0.239,-1.711,1.261,-0.19,-1.815,0.032,-1.28,-1.172,1.891,-2.416,-0.661,1.127,-3.548,-0.217,2.056,-1.964,0.529,0.276,-2.364,0.659,-0.88,-1.13,1.391,0.856,-0.62,2.565,0.148,0.228,3.439,1.077,0.231,2.129,-1.032,0.179,2.733,-2.099,1.028,1.084,-0.833,1.872,0.593,-1.919,2.85,-0.462,-1.397,1.02,0.02,-3.049,1.317,0.227,-4.224,-0.051,-0.684,-2.696,-0.927,-1.261,-3.713,-1.933,-2.219,-3.074,-1.663,-0.171,-4.475,-1.916,-0.296,-5.673
H5_ltThe LESS_THAN action with label H5_lt calculates the following quantities:| Quantity | Type | Description |
| H5_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=H5_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
H5The SUM action with label H5 calculates the following quantities:| Quantity | Type | Description |
| H5 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=H5_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=path_cmap.dat
# INCLUDE FILE=path_cmap.dat
The INCLUDE action with label path_cmap.dat calculates somethingCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=3468,3080 REFERENCE1A reference value for a given contact, by default is 0=0.97915123 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458 REFERENCE2A reference value for a given contact, by default is 0=0.00041408 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438 REFERENCE3A reference value for a given contact, by default is 0=0.02647680 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438 REFERENCE4A reference value for a given contact, by default is 0=0.08877594 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951 REFERENCE5A reference value for a given contact, by default is 0=0.42785568 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387 REFERENCE6A reference value for a given contact, by default is 0=0.10367204 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936 REFERENCE7A reference value for a given contact, by default is 0=0.98727453 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625 REFERENCE8A reference value for a given contact, by default is 0=0.14748926 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c1The CONTACTMAP action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | scalar | the sum of all the switching function on all the distances |
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=3468,3080 REFERENCE1A reference value for a given contact, by default is 0=0.99076543 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458 REFERENCE2A reference value for a given contact, by default is 0=0.00120232 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438 REFERENCE3A reference value for a given contact, by default is 0=0.07366488 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438 REFERENCE4A reference value for a given contact, by default is 0=0.79523553 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951 REFERENCE5A reference value for a given contact, by default is 0=0.28660977 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387 REFERENCE6A reference value for a given contact, by default is 0=0.33348235 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936 REFERENCE7A reference value for a given contact, by default is 0=0.96457138 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625 REFERENCE8A reference value for a given contact, by default is 0=0.12877288 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c2The CONTACTMAP action with label c2 calculates the following quantities:| Quantity | Type | Description |
| c2 | scalar | the sum of all the switching function on all the distances |
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=3468,3080 REFERENCE1A reference value for a given contact, by default is 0=0.97985636 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458 REFERENCE2A reference value for a given contact, by default is 0=0.00298822 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438 REFERENCE3A reference value for a given contact, by default is 0=0.32581507 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438 REFERENCE4A reference value for a given contact, by default is 0=0.97691480 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951 REFERENCE5A reference value for a given contact, by default is 0=0.64179803 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387 REFERENCE6A reference value for a given contact, by default is 0=0.39343434 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936 REFERENCE7A reference value for a given contact, by default is 0=0.80857049 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625 REFERENCE8A reference value for a given contact, by default is 0=0.98023826 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c3The CONTACTMAP action with label c3 calculates the following quantities:| Quantity | Type | Description |
| c3 | scalar | the sum of all the switching function on all the distances |
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=3468,3080 REFERENCE1A reference value for a given contact, by default is 0=0.98302451 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458 REFERENCE2A reference value for a given contact, by default is 0=0.00222719 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438 REFERENCE3A reference value for a given contact, by default is 0=0.28721980 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438 REFERENCE4A reference value for a given contact, by default is 0=0.97341515 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951 REFERENCE5A reference value for a given contact, by default is 0=0.39377719 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387 REFERENCE6A reference value for a given contact, by default is 0=0.58032321 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936 REFERENCE7A reference value for a given contact, by default is 0=0.10151712 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625 REFERENCE8A reference value for a given contact, by default is 0=0.99945112 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c4The CONTACTMAP action with label c4 calculates the following quantities:| Quantity | Type | Description |
| c4 | scalar | the sum of all the switching function on all the distances |
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=3468,3080 REFERENCE1A reference value for a given contact, by default is 0=0.37447568 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458 REFERENCE2A reference value for a given contact, by default is 0=0.00700306 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438 REFERENCE3A reference value for a given contact, by default is 0=0.47787638 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438 REFERENCE4A reference value for a given contact, by default is 0=0.97674738 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951 REFERENCE5A reference value for a given contact, by default is 0=0.03917644 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387 REFERENCE6A reference value for a given contact, by default is 0=0.99881752 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936 REFERENCE7A reference value for a given contact, by default is 0=0.00122655 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625 REFERENCE8A reference value for a given contact, by default is 0=0.99974666 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c5The CONTACTMAP action with label c5 calculates the following quantities:| Quantity | Type | Description |
| c5 | scalar | the sum of all the switching function on all the distances |
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=3468,3080 REFERENCE1A reference value for a given contact, by default is 0=0.00478415 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458 REFERENCE2A reference value for a given contact, by default is 0=0.37643526 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438 REFERENCE3A reference value for a given contact, by default is 0=0.96181240 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438 REFERENCE4A reference value for a given contact, by default is 0=0.96500778 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951 REFERENCE5A reference value for a given contact, by default is 0=0.16431360 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387 REFERENCE6A reference value for a given contact, by default is 0=0.98327651 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936 REFERENCE7A reference value for a given contact, by default is 0=0.28874741 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625 REFERENCE8A reference value for a given contact, by default is 0=0.96352033 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c6The CONTACTMAP action with label c6 calculates the following quantities:| Quantity | Type | Description |
| c6 | scalar | the sum of all the switching function on all the distances |
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=3468,3080 REFERENCE1A reference value for a given contact, by default is 0=0.00064458 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458 REFERENCE2A reference value for a given contact, by default is 0=0.93811079 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438 REFERENCE3A reference value for a given contact, by default is 0=0.99043541 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438 REFERENCE4A reference value for a given contact, by default is 0=0.96998468 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951 REFERENCE5A reference value for a given contact, by default is 0=0.03311838 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387 REFERENCE6A reference value for a given contact, by default is 0=0.99966434 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936 REFERENCE7A reference value for a given contact, by default is 0=0.06060704 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625 REFERENCE8A reference value for a given contact, by default is 0=0.99816484 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c7The CONTACTMAP action with label c7 calculates the following quantities:| Quantity | Type | Description |
| c7 | scalar | the sum of all the switching function on all the distances |
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP
# --- End of included input --- p1The FUNCPATHMSD action with label p1 calculates the following quantities:| Quantity | Type | Description |
| p1.s | scalar | the position on the path |
| p1.z | scalar | the distance from the path |
: FUNCPATHMSDThis function calculates path collective variables. More details ARGthe labels of the values from which the function is calculated=c1,c2,c3,c4,c5,c6,c7 LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=3.634
metaThe METAD action with label meta calculates the following quantities:| Quantity | Type | Description |
| meta.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=p.sss,p1.s SIGMAthe widths of the Gaussian hills=0.1,0.03 HEIGHTthe heights of the Gaussian hills=4 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=1,1 GRID_MAXthe upper bounds for the grid=12,7 GRID_WFILEthe file on which to write the grid=GRID_W GRID_WSTRIDEwrite the grid to a file every N steps=2500000
meta: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=p.sss,p1.s SIGMAthe widths of the Gaussian hills=0.1,0.03 HEIGHTthe heights of the Gaussian hills=4 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=1,1 GRID_MAXthe upper bounds for the grid=12,7 GRID_WFILEthe file on which to write the grid=GRID_W GRID_WSTRIDEwrite the grid to a file every N steps=2500000 FILE a file in which the list of added hills is stored=HILLS
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:| Quantity | Type | Description |
| lwall.bias | scalar | the instantaneous value of the bias potential |
| lwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=H6 ATthe positions of the wall=24.8 KAPPAthe force constant for the wall=1500.0
d3The DISTANCE action with label d3 calculates the following quantities:| Quantity | Type | Description |
| d3 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1519,3047
d4The DISTANCE action with label d4 calculates the following quantities:| Quantity | Type | Description |
| d4 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1469,2989
d5The DISTANCE action with label d5 calculates the following quantities:| Quantity | Type | Description |
| d5 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1414,2909
uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities:| Quantity | Type | Description |
| uwall1.bias | scalar | the instantaneous value of the bias potential |
| uwall1.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d3 ATthe positions of the wall=0.75 KAPPAthe force constant for the wall=100.000
uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities:| Quantity | Type | Description |
| uwall2.bias | scalar | the instantaneous value of the bias potential |
| uwall2.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d4 ATthe positions of the wall=0.625 KAPPAthe force constant for the wall=100.000
uwall3The UPPER_WALLS action with label uwall3 calculates the following quantities:| Quantity | Type | Description |
| uwall3.bias | scalar | the instantaneous value of the bias potential |
| uwall3.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d5 ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=100.000
uwallpzThe UPPER_WALLS action with label uwallpz calculates the following quantities:| Quantity | Type | Description |
| uwallpz.bias | scalar | the instantaneous value of the bias potential |
| uwallpz.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.z ATthe positions of the wall=0.05 KAPPAthe force constant for the wall=1000.0
d6The DISTANCE action with label d6 calculates the following quantities:| Quantity | Type | Description |
| d6 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2936,4418
uwThe UPPER_WALLS action with label uw calculates the following quantities:| Quantity | Type | Description |
| uw.bias | scalar | the instantaneous value of the bias potential |
| uw.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d6 ATthe positions of the wall=0.65 KAPPAthe force constant for the wall=00.000
d7The DISTANCE action with label d7 calculates the following quantities:| Quantity | Type | Description |
| d7 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3468,3332
lwThe LOWER_WALLS action with label lw calculates the following quantities:| Quantity | Type | Description |
| lw.bias | scalar | the instantaneous value of the bias potential |
| lw.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d7 ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=100.00
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR
