Project ID: plumID:23.045
Source: Path-CVs_MetaD/apo/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
=FApo.pdb
The MOLINFO action with label calculates somethingp: =path_rmsd.pdb =100.00
The PATHMSD action with label p calculates the following quantities: Quantity | Description |
p.sss | the position on the path |
p.zzz | the distance from the path |
d1: =1458,3468
The DISTANCE action with label d1 calculates the following quantities: Quantity | Description |
d1.value | the DISTANCE between this pair of atoms |
d2: =3080,3468
The DISTANCE action with label d2 calculates the following quantities: Quantity | Description |
d2.value | the DISTANCE between this pair of atoms |
H6: =220-252
The ALPHARMSD action with label H6 calculates the following quantities: Quantity | Description |
H6.struct | the vectors containing the rmsd distances between the residues and each of the reference structures |
H6.lessthan | the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold |
H6: =220-252 =8 =0.0 =12 =DRMSD
# H6: ALPHARMSD RESIDUES=220-252
H6_rmsd: =0.17 =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 =DRMSD =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 =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 =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 =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 =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 =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
The SECONDARY_STRUCTURE_RMSD action with label H6_rmsd calculates the following quantities: Quantity | Description |
H6_rmsd.struct | the vectors containing the rmsd distances between the residues and each of the reference structures |
H6_rmsd.lessthan | the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold |
H6_lt: =H6_rmsd ={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
The LESS_THAN action with label H6_lt calculates the following quantities: Quantity | Description |
H6_lt.value | a function that is one if the input is less than a threshold |
H6: =H6_lt =NO
# --- End of included input --- H5: =198-209
The ALPHARMSD action with label H5 calculates the following quantities: Quantity | Description |
H5.struct | the vectors containing the rmsd distances between the residues and each of the reference structures |
H5.lessthan | the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold |
H5: =198-209 =8 =0.0 =12 =DRMSD
# H5: ALPHARMSD RESIDUES=198-209
H5_rmsd: =0.17 =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 =DRMSD =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 =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 =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 =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 =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 =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
The SECONDARY_STRUCTURE_RMSD action with label H5_rmsd calculates the following quantities: Quantity | Description |
H5_rmsd.struct | the vectors containing the rmsd distances between the residues and each of the reference structures |
H5_rmsd.lessthan | the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold |
H5_lt: =H5_rmsd ={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
The LESS_THAN action with label H5_lt calculates the following quantities: Quantity | Description |
H5_lt.value | a function that is one if the input is less than a threshold |
H5: =H5_lt =NO
# --- End of included input ---
=path_cmap.dat
# INCLUDE FILE=path_cmap.dat
The INCLUDE action with label path_cmap.dat calculates something ...
=3468,3080 =0.97915123 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1458 =0.00041408 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1438 =0.02647680 ={RATIONAL R_0=1.65 NN=8 MM=18}
=1458,1438 =0.08877594 ={RATIONAL R_0=0.75 NN=6 MM=18}
=3566,2951 =0.42785568 ={RATIONAL R_0=0.90 NN=8 MM=16}
=3566,1387 =0.10367204 ={RATIONAL R_0=1.00 NN=10 MM=24}
=4418,2936 =0.98727453 ={RATIONAL R_0=0.85 NN=8 MM=28}
=4418,624 =0.14748926 ={RATIONAL R_0=0.67 NN=12 MM=24}
=c1
... CONTACTMAP
The CONTACTMAP action with label c1 calculates the following quantities: Quantity | Description |
c1.contact | By not using SUM or CMDIST each contact will be stored in a component |
...
=3468,3080 =0.99076543 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1458 =0.00120232 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1438 =0.07366488 ={RATIONAL R_0=1.65 NN=8 MM=18}
=1458,1438 =0.79523553 ={RATIONAL R_0=0.75 NN=6 MM=18}
=3566,2951 =0.28660977 ={RATIONAL R_0=0.90 NN=8 MM=16}
=3566,1387 =0.33348235 ={RATIONAL R_0=1.00 NN=10 MM=24}
=4418,2936 =0.96457138 ={RATIONAL R_0=0.85 NN=8 MM=28}
=4418,624 =0.12877288 ={RATIONAL R_0=0.67 NN=12 MM=24}
=c2
... CONTACTMAP
The CONTACTMAP action with label c2 calculates the following quantities: Quantity | Description |
c2.contact | By not using SUM or CMDIST each contact will be stored in a component |
...
=3468,3080 =0.97985636 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1458 =0.00298822 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1438 =0.32581507 ={RATIONAL R_0=1.65 NN=8 MM=18}
=1458,1438 =0.97691480 ={RATIONAL R_0=0.75 NN=6 MM=18}
=3566,2951 =0.64179803 ={RATIONAL R_0=0.90 NN=8 MM=16}
=3566,1387 =0.39343434 ={RATIONAL R_0=1.00 NN=10 MM=24}
=4418,2936 =0.80857049 ={RATIONAL R_0=0.85 NN=8 MM=28}
=4418,624 =0.98023826 ={RATIONAL R_0=0.67 NN=12 MM=24}
=c3
... CONTACTMAP
The CONTACTMAP action with label c3 calculates the following quantities: Quantity | Description |
c3.contact | By not using SUM or CMDIST each contact will be stored in a component |
...
=3468,3080 =0.98302451 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1458 =0.00222719 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1438 =0.28721980 ={RATIONAL R_0=1.65 NN=8 MM=18}
=1458,1438 =0.97341515 ={RATIONAL R_0=0.75 NN=6 MM=18}
=3566,2951 =0.39377719 ={RATIONAL R_0=0.90 NN=8 MM=16}
=3566,1387 =0.58032321 ={RATIONAL R_0=1.00 NN=10 MM=24}
=4418,2936 =0.10151712 ={RATIONAL R_0=0.85 NN=8 MM=28}
=4418,624 =0.99945112 ={RATIONAL R_0=0.67 NN=12 MM=24}
=c4
... CONTACTMAP
The CONTACTMAP action with label c4 calculates the following quantities: Quantity | Description |
c4.contact | By not using SUM or CMDIST each contact will be stored in a component |
...
=3468,3080 =0.37447568 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1458 =0.00700306 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1438 =0.47787638 ={RATIONAL R_0=1.65 NN=8 MM=18}
=1458,1438 =0.97674738 ={RATIONAL R_0=0.75 NN=6 MM=18}
=3566,2951 =0.03917644 ={RATIONAL R_0=0.90 NN=8 MM=16}
=3566,1387 =0.99881752 ={RATIONAL R_0=1.00 NN=10 MM=24}
=4418,2936 =0.00122655 ={RATIONAL R_0=0.85 NN=8 MM=28}
=4418,624 =0.99974666 ={RATIONAL R_0=0.67 NN=12 MM=24}
=c5
... CONTACTMAP
The CONTACTMAP action with label c5 calculates the following quantities: Quantity | Description |
c5.contact | By not using SUM or CMDIST each contact will be stored in a component |
...
=3468,3080 =0.00478415 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1458 =0.37643526 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1438 =0.96181240 ={RATIONAL R_0=1.65 NN=8 MM=18}
=1458,1438 =0.96500778 ={RATIONAL R_0=0.75 NN=6 MM=18}
=3566,2951 =0.16431360 ={RATIONAL R_0=0.90 NN=8 MM=16}
=3566,1387 =0.98327651 ={RATIONAL R_0=1.00 NN=10 MM=24}
=4418,2936 =0.28874741 ={RATIONAL R_0=0.85 NN=8 MM=28}
=4418,624 =0.96352033 ={RATIONAL R_0=0.67 NN=12 MM=24}
=c6
... CONTACTMAP
The CONTACTMAP action with label c6 calculates the following quantities: Quantity | Description |
c6.contact | By not using SUM or CMDIST each contact will be stored in a component |
...
=3468,3080 =0.00064458 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1458 =0.93000000 ={RATIONAL R_0=0.70 NN=8 MM=16}
=3468,1438 =0.99043541 ={RATIONAL R_0=1.65 NN=8 MM=18}
=1458,1438 =0.96998468 ={RATIONAL R_0=0.75 NN=6 MM=18}
=3566,2951 =0.03311838 ={RATIONAL R_0=0.90 NN=8 MM=16}
=3566,1387 =0.99966434 ={RATIONAL R_0=1.00 NN=10 MM=24}
=4418,2936 =0.06060704 ={RATIONAL R_0=0.85 NN=8 MM=28}
=4418,624 =0.99816484 ={RATIONAL R_0=0.67 NN=12 MM=24}
=c7
... CONTACTMAP
# --- End of included input --- The CONTACTMAP action with label c7 calculates the following quantities: Quantity | Description |
c7.contact | By not using SUM or CMDIST each contact will be stored in a component |
p1: =c1,c2,c3,c4,c5,c6,c7 =3.634
The FUNCPATHMSD action with label p1 calculates the following quantities: Quantity | Description |
p1.s | the position on the path |
p1.z | the distance from the path |
meta: =p.sss,p1.s =0.1,0.03 =4 =1000 =15 =300 =1,1 =12,7 =GRID_W =2500000
The METAD action with label meta calculates the following quantities: Quantity | Description |
meta.bias | the instantaneous value of the bias potential |
meta: =p.sss,p1.s =0.1,0.03 =4 =1000 =15 =300 =1,1 =12,7 =GRID_W =2500000 =HILLS
lwall: =H6 =24.8 =1500.0
The LOWER_WALLS action with label lwall calculates the following quantities: Quantity | Description |
lwall.bias | the instantaneous value of the bias potential |
lwall.force2 | the instantaneous value of the squared force due to this bias potential |
d3: =1519,3047
The DISTANCE action with label d3 calculates the following quantities: Quantity | Description |
d3.value | the DISTANCE between this pair of atoms |
d4: =1469,2989
The DISTANCE action with label d4 calculates the following quantities: Quantity | Description |
d4.value | the DISTANCE between this pair of atoms |
d5: =1414,2909
The DISTANCE action with label d5 calculates the following quantities: Quantity | Description |
d5.value | the DISTANCE between this pair of atoms |
uwall1: =d3 =0.75 =100.000
The UPPER_WALLS action with label uwall1 calculates the following quantities: Quantity | Description |
uwall1.bias | the instantaneous value of the bias potential |
uwall1.force2 | the instantaneous value of the squared force due to this bias potential |
uwall2: =d4 =0.625 =100.000
The UPPER_WALLS action with label uwall2 calculates the following quantities: Quantity | Description |
uwall2.bias | the instantaneous value of the bias potential |
uwall2.force2 | the instantaneous value of the squared force due to this bias potential |
uwall3: =d5 =0.7 =100.000
The UPPER_WALLS action with label uwall3 calculates the following quantities: Quantity | Description |
uwall3.bias | the instantaneous value of the bias potential |
uwall3.force2 | the instantaneous value of the squared force due to this bias potential |
uwallpz: =p1.z =0.05 =1000.0
The UPPER_WALLS action with label uwallpz calculates the following quantities: Quantity | Description |
uwallpz.bias | the instantaneous value of the bias potential |
uwallpz.force2 | the instantaneous value of the squared force due to this bias potential |
d6: =2936,4418
The DISTANCE action with label d6 calculates the following quantities: Quantity | Description |
d6.value | the DISTANCE between this pair of atoms |
uw: =d6 =0.65 =00.000
The UPPER_WALLS action with label uw calculates the following quantities: Quantity | Description |
uw.bias | the instantaneous value of the bias potential |
uw.force2 | the instantaneous value of the squared force due to this bias potential |
d7: =3468,3332
The DISTANCE action with label d7 calculates the following quantities: Quantity | Description |
d7.value | the DISTANCE between this pair of atoms |
lw: =d7 =0.7 =100.00
The LOWER_WALLS action with label lw calculates the following quantities: Quantity | Description |
lw.bias | the instantaneous value of the bias potential |
lw.force2 | the instantaneous value of the squared force due to this bias potential |
=1000 =COLVAR