Project ID: plumID:19.039
Source: plumed.dat
Originally used with PLUMED version: 2.6-dev
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 onv2.9
tested onmaster
#RESTART

# To be used to force reconstruction of periodic boundary conditions

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=54,75,212,228,239,258,311,328,348,372,383,402,421,463,487,503,519,657,674,690,714,897,914,934,953,964,974,985,1007,1018,1037,1247,1264,1283,1302,1324,1689,1708,1727,1738,1962,1984,1994,2312,2329,2349,2467,2490,2500,2517,2524,2536,2547,2554,2569,2575,2591,2607,2635,2657,2676,2693,2700,2719,2735,2746,2770,2777,2788,2795,2805,2815,2832,2854,2868,2898,2904,2911,2927,2948,2962,2472,3221,3224,3225,3228,3229,3231,3233,3235,3237

d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2472,3224
lig: 
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
=3221,3224,3225,3228,3229,3231,3233,3235,3237

# This collective variable has the information of the position of the ligand with respect to the funnel-shape restraint potential. The reference file specified in REFERENCE should contain only the target molecule (no ligand, solvent, ecc.)
fps: 
FUNNEL_PS
FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More details
 
LIGAND
This MUST be a single atom, normally the COM of the ligand
=lig 
REFERENCE
a file in pdb format containing the structure you would like to align
=start.pdb 
ANCHOR
Closest protein atom to the ligand, picked to avoid pbc problems during the simulation
=2472 
POINTS
6 values defining x, y, and z of the 2 points used to construct the line
=4.724,5.369,4.069,4.597,5.721,4.343

rmsd: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=start.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

# If not already present, FUNNEL will create the funnel potential and write it to the file specified in FILE

FUNNEL
Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=fps.lp,fps.ld 
ZCC
 switching point between cylinder and cone
=1.8 
ALPHA
angle to change the width of the cone section
=0.55 
RCYL
radius of the cylindrical section
=0.1 
MINS
minimum value assumed by fps
=-0.5 
MAXS
 maximum value assumed by fps
=3.7 
KAPPA
constant to be used for the funnel-shape restraint potential
=35100 
NBINS
number of bins along fps
=500 
NBINZ
number of bins along fps
=500 
FILE
name of the Funnel potential file
=BIAS 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=funnel

# remove BIASFACTOR if you want to perform standard metadynamics

METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1 
SIGMA
the widths of the Gaussian hills
=0.01 
HEIGHT
the heights of the Gaussian hills
=2.0 
PACE
the frequency for hill addition
=500 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad 
GRID_MIN
the lower bounds for the grid
=0.0 
GRID_MAX
the upper bounds for the grid
=4.0 
GRID_WFILE
the file on which to write the grid
=grid_w.dat 
GRID_WSTRIDE
write the grid to a file every N steps
=250000

LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=fps.lp 
AT
the positions of the wall
=-0.3 
KAPPA
the force constant for the wall
=500000 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall

UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=rmsd 
AT
the positions of the wall
=0.09 
KAPPA
the force constant for the wall
=500000 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall-rmsd

UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=fps.lp 
AT
the positions of the wall
=3.4 
KAPPA
the force constant for the wall
=500000 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall

UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d1 
AT
the positions of the wall
=3.8 
KAPPA
the force constant for the wall
=500000 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=distwall

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR