PLUMED-NEST

Project ID: plumID:23.025
Source: cylinder_metadynamics/3ibk/terra_metady_cyl_K1.dat
Originally used with PLUMED version: 2.7
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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A # modify the default length unit (nm) to Angstrom and energy to kcal/mol

The UNITS action with label  calculates something
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
=1-1520,35634     # atoms of receptor and ligand
FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=3ibk_tetradcore.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL # pdb with reference atoms to fit


#######################################3
# Defining groups and binding site
Klig: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=35634    # K bulk ion that will serve as ligand
The GROUP action with label Klig calculates somethingK1: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1517       # K1 ion that will serve as binding site reference
The GROUP action with label K1 calculates somethingK2: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1519       # K2 ion that will serve as binding site reference

The GROUP action with label K2 calculates somethingtetrad1: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=132-161,511-540,890-919,1269-1298    # GUA base atoms
The GROUP action with label tetrad1 calculates somethingtetrad2: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=198-227,577-606,956-985,1335-1364    # GUA base atoms
The GROUP action with label tetrad2 calculates somethingtetrad3: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=264-293,643-672,1022-1051,1401-1430  # GUA base atoms

The GROUP action with label tetrad3 calculates somethingsite1: 
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
=tetrad3,tetrad2        # region of K1 ion that will serve as binding site reference
The COM action with label site1 calculates somethingsite2: 
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
=tetrad1,tetrad2        # region of K2 ion that will serve as binding site reference

The COM action with label site2 calculates somethingKBULK: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=35596,35598,35600,35602,35604,35606,35608,35610,35612,35614,35616,35618,35620,35622,35624,35626,35628,35630,35632,35636,35638,35640,35642,35644,35646,35648,35650,35652,35654 # K bulk ions

The GROUP action with label KBULK calculates somethingcheck_site1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=K1,site1
The DISTANCE action with label check_site1 calculates the following quantities:
 Quantity   
 Description  
check_site1.value
the DISTANCE between this pair of atomscheck_site2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=K2,site2

The DISTANCE action with label check_site2 calculates the following quantities:
 Quantity   
 Description  
check_site2.value
the DISTANCE between this pair of atoms
WRAPAROUND
Rebuild periodic boundary conditions around chosen atoms. More details
 
ATOMS
wrapped atoms
=Klig 
AROUND
reference atoms
=tetrad1,tetrad2,tetrad3

#######################################
# Creating KBULK binding restraints to K1 and K2
# to prevent ion binding competition

mindist1: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=K1 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=KBULK 
LOWEST
 this flag allows you to recover the lowest of these variables
The DISTANCES action with label mindist1 calculates somethingrepulsivewall1: 
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
=mindist1.lowest 
AT
the positions of the wall
=6.0 
KAPPA
the force constant for the wall
=2000.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0

The LOWER_WALLS action with label repulsivewall1 calculates somethingmindist2: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=K2 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=KBULK 
LOWEST
 this flag allows you to recover the lowest of these variables
The DISTANCES action with label mindist2 calculates somethingrepulsivewall2: 
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
=mindist2.lowest 
AT
the positions of the wall
=6.0 
KAPPA
the force constant for the wall
=2000.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0

#######################################
# Build the cylinder using site1 and Klig coordinates

The LOWER_WALLS action with label repulsivewall2 calculates somethingKlig_coord: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=Klig 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The POSITION action with label Klig_coord calculates the following quantities:
 Quantity   
 Description  
Klig_coord.x
the x-component of the atom position
Klig_coord.y
the y-component of the atom position
Klig_coord.z
the z-component of the atom positionsite1_coord: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=site1 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# calculating the distance from site1 to Klig
The POSITION action with label site1_coord calculates the following quantities:
 Quantity   
 Description  
site1_coord.x
the x-component of the atom position
site1_coord.y
the y-component of the atom position
site1_coord.z
the z-component of the atom positiond1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=Klig,site1 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label

# distances for each cartesian component
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atoms
d1.value
the DISTANCE between this pair of atomsabs_x: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=Klig_coord.x,site1_coord.x 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label abs_x calculates somethingabs_y: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=Klig_coord.y,site1_coord.y 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label abs_y calculates somethingabs_z: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=Klig_coord.z,site1_coord.z 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Defining cylinder via descriptive coordinates
The MATHEVAL action with label abs_z calculates somethingrho: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs_x,abs_y 
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label rho calculates somethingphi: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs_x,abs_y 
FUNC
the function you wish to evaluate
=atan2(y,x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-pi,pi

# restraining cylinder lateral size
The MATHEVAL action with label phi calculates somethingcylrestr1: 
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
=rho 
AT
the positions of the wall
=7.0 
KAPPA
the force constant for the wall
=5000        # controls the maximum cylinder radius - 0.7 nm in this case

# restraining K1 from transpassing the cylinder heights
The UPPER_WALLS action with label cylrestr1 calculates somethingcylrestr2: 
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
=d1.z 
AT
the positions of the wall
=1.5  
KAPPA
the force constant for the wall
=2500      # controls the maximum cylinder height. IMPORTANT - this must be a LOWER_WALLs if your binding site is at a negative Z region
The LOWER_WALLS action with label cylrestr2 calculates somethingcylrestr3: 
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.z 
AT
the positions of the wall
=22.0 
KAPPA
the force constant for the wall
=2500      # controls the minimum cylinder height. IMPORTANT - this must be a UPPER_WALLs if your binding site is at a negative Z region

########################################
# Defining CV and metadynamics procedures

The UPPER_WALLS action with label cylrestr3 calculates somethingd1real: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=Klig,K1
The DISTANCE action with label d1real calculates the following quantities:
 Quantity   
 Description  
d1real.value
the DISTANCE between this pair of atomsd1real_xyz: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=Klig,K1 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label

The DISTANCE action with label d1real_xyz calculates the following quantities:
 Quantity   
 Description  
d1real_xyz.x
the x-component of the vector connecting the two atoms
d1real_xyz.y
the y-component of the vector connecting the two atoms
d1real_xyz.z
the z-component of the vector connecting the two atoms
d1real_xyz.value
the DISTANCE between this pair of atomsthetax: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs_x,d1real 
FUNC
the function you wish to evaluate
=asin(x/y)*(180/pi 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label thetax calculates somethingthetay: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs_y,d1real 
FUNC
the function you wish to evaluate
=asin(x/y)*(180/pi 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO


The MATHEVAL action with label thetay calculates somethingmetad: 
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.z,rho,phi 
SIGMA
the widths of the Gaussian hills
=0.5,0.5,pi/8 
HEIGHT
the heights of the Gaussian hills
=1.0 
PACE
the frequency for hill addition
=500 
FILE
 a file in which the list of added hills is stored
=HILLS_CYL 
GRID_MIN
the lower bounds for the grid
=0.0,0.0,-pi 
GRID_MAX
the upper bounds for the grid
=25.0,10.0,pi 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298

########################################
# Printing arguments
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=COLVAR_CYL
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1.z,d1real,d1real_xyz.z 
FILE
the name of the file on which to output these quantities
=distance.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=metad 
FILE
the name of the file on which to output these quantities
=metad_data.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cylrestr1.*,cylrestr2.*,cylrestr3 
FILE
the name of the file on which to output these quantities
=cylinder_restraint.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=mindist1.lowest,repulsivewall1.*,mindist2.lowest,repulsivewall2 
FILE
the name of the file on which to output these quantities
=repulsivewalls.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=abs_x,abs_y,abs_z 
FILE
the name of the file on which to output these quantities
=xyz_coord.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rho,d1.z,phi 
FILE
the name of the file on which to output these quantities
=rdp_coord.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=thetax,thetay 
FILE
the name of the file on which to output these quantities
=angles.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=check_site1,check_site2 
FILE
the name of the file on which to output these quantities
=check_site.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
DUMPATOMS
Dump selected atoms on a file. More details
 
STRIDE
 the frequency with which the atoms should be output
=1000 
FILE
file on which to output coordinates; extension is automatically detected
=lig_coords.gro 
ATOMS
the atom indices whose positions you would like to print out
=Klig

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1000