Project ID: plumID:21.022
Source: SiNP_Car9/plumed.dat
Originally used with PLUMED version: 2.4
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
tested onv2.8
tested onmaster
## RESTART

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
MOLTYPE
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein
STRUCTURE
a file in pdb format containing a reference structure
=car9_ACE_NME.pdb
ENERGY
Calculate the total potential energy of the simulation box. More details
LABEL
a label for the action so that its output can be referenced in the input to other actions
=energy
ncap:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11713-11718 ccap:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11914-11919
bb:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11717,11718,11719,11729,11730,11731,11740,11741,11742,11750,11751,11752,11774,11775,11776,11781,11782,11783,11801,11802,11803,11823,11824,11825,11845,11846,11847,11859,11860,11861,11866,11867,11868,11888,11889,11890,11912,11913,11914
asp:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11720-11728 ser:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11732-11739 ala:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11743-11749 arg:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11753-11773 gly:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11777-11780 phe:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11784-11800 lys:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11804-11822 lys2:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11826-11844 pro:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11848-11858 gly2:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11862-11865 lys3:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11869-11887 arg2:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=11891-11911
top_oh:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=78,177,385,439,459,497,570,601,634,637,640,643,644,648,653,660,662,684,709,734,795,898,1036,1041,1110,1184,1222,1295,1328,1365,1368,1371,1373,1376,1377,1382,1389,1412,1438,1521,1620,1759,1829,1883,1903,1941,2014,2042,2046,2079,2082,2085,2087,2089,2093,2098,2105,2106,2107,2128,2153,2156,2183,2244,2347,2490,2560,2614,2634,2672,2745,2778,2815,2818,2821,2823,2826,2827,2832,2838,2861,2886,2892,2908,3006,3105,3313,3367,3387,3425,3498,3529,3562,3565,3568,3571,3572,3576,3581,3588,3590,3612,3637,3662,3723,3826,3964,3969,4038,4112,4150,4223,4256,4293,4296,4299,4301,4304,4305,4310,4317,4340,4366,4449,4548,4687,4757,4811,4831,4869,4942,4970,4974,5007,5010,5013,5015,5017,5021,5026,5033,5034,5035,5056,5081,5084,5111,5172,5275,5418,5488,5542,5562,5600,5673,5706,5743,5746,5749,5751,5754,5755,5760,5766,5789,5814,5820,5836,5934,6033,6241,6295,6315,6353,6426,6457,6490,6493,6496,6499,6500,6504,6509,6516,6518,6540,6565,6590,6651,6754,6892,6897,6966,7040,7078,7151,7184,7221,7224,7227,7229,7232,7233,7238,7245,7268,7294,7377,7476,7615,7685,7739,7759,7797,7870,7898,7902,7935,7938,7941,7943,7945,7949,7954,7961,7962,7963,7984,8009,8012,8039,8100,8203,8346,8416,8470,8490,8528,8601,8634,8671,8674,8677,8679,8682,8683,8688,8694,8717,8742,8748,8764,8862,8961,9169,9223,9243,9281,9354,9385,9418,9421,9424,9427,9428,9432,9437,9444,9446,9468,9493,9518,9579,9682,9820,9825,9894,9968,10006,10079,10112,10149,10152,10155,10157,10160,10161,10166,10173,10196,10222,10305,10404,10543,10613,10667,10687,10725,10798,10826,10830,10863,10866,10869,10871,10873,10877,10882,10889,10890,10891,10912,10937,10940,10967,11028,11131,11274,11344,11398,11418,11456,11529,11562,11599,11602,11605,11607,11610,11611,11616,11622,11645,11670,11676,11692
dcaps:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=ncap,ccap dncap:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ncap
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dccap:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ccap
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances

dbb:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,bb
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dasp:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,asp
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dser:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ser
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dala:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ala
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
darg:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,arg
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dgly:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,gly
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dphe:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,phe
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dlys:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,lys
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dlys2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,lys2
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dpro:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,pro
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dgly2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,gly2
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
dlys3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,lys3
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
darg2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,arg2
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances

LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dcaps
AT
the positions of the wall
=0.8
KAPPA
the force constant for the wall
=100000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dcaps_min
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dcaps
AT
the positions of the wall
=1.8
KAPPA
the force constant for the wall
=100000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dcaps_max
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dncap.z
AT
the positions of the wall
=0.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dncap_min
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dccap.z
AT
the positions of the wall
=0.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dccap_min
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dbb.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dbb
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dasp.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dasp
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dser.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dser
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dala.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dala
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=darg.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_darg
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dgly.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dgly
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dphe.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dphe
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dlys.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dlys
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dlys2.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dlys2
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dpro.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dpro
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dgly2.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dgly2
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=dlys3.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dlys3
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=darg2.z
AT
the positions of the wall
=6.5
KAPPA
the force constant for the wall
=1000000
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_darg2
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
TYPE
The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=11713-11919
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rg
PBMETAD
Used to performed Parallel Bias metadynamics. More details
...
WALKERS_MPI
Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
ARG
the input for this action is the scalar output from one or more other actions
=dbb.z,dasp.z,dser.z,dala.z,darg.z,dgly.z,dphe.z,dlys.z,dlys2.z,dpro.z,dgly2.z,dlys3.z,darg2.z,rg
SIGMA
the widths of the Gaussian hills
=0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2 #kJ/mol
PACE
the frequency for hill addition, one for all biases
=1000
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=20
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=PBMETAD
GRID_MIN
the lower bounds for the grid
=-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0
GRID_MAX
the upper bounds for the grid
=9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,8
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS.dbb,HILLS.dasp,HILLS.dser,HILLS.dala,HILLS.darg,HILLS.dgly,HILLS.dphe,HILLS.dlys,HILLS.dlys2,HILLS.dpro,HILLS.dgly2,HILLS.dlys3,HILLS.darg2,HILLS.rg ... PBMETAD
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=dcaps,dbb.z,dncap.z,dccap.z,dasp.z,dser.z,dala.z,darg.z,dgly.z,dphe.z,dlys.z,dlys2.z,dpro.z,dgly2.z,dlys3.z,darg2.z,rg,energy,PBMETAD.bias
STRIDE
the frequency with which the quantities of interest should be output
=500
FILE
the name of the file on which to output these quantities
=COLVAR