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

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

The UNITS action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-1520,35634     # atoms of receptor and ligand
FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa 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
KligThe GROUP action with label Klig calculates the following quantities:
 Quantity   
 Type   
 Description  
Klig
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=35634    # K bulk ion that will serve as ligand
K1The GROUP action with label K1 calculates the following quantities:
 Quantity   
 Type   
 Description  
K1
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1517       # K1 ion that will serve as binding site reference
K2The GROUP action with label K2 calculates the following quantities:
 Quantity   
 Type   
 Description  
K2
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1519       # K2 ion that will serve as binding site reference

tetrad1The GROUP action with label tetrad1 calculates the following quantities:
 Quantity   
 Type   
 Description  
tetrad1
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=132-161,511-540,890-919,1269-1298    # GUA base atoms
tetrad2The GROUP action with label tetrad2 calculates the following quantities:
 Quantity   
 Type   
 Description  
tetrad2
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=198-227,577-606,956-985,1335-1364    # GUA base atoms
tetrad3The GROUP action with label tetrad3 calculates the following quantities:
 Quantity   
 Type   
 Description  
tetrad3
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=264-293,643-672,1022-1051,1401-1430  # GUA base atoms

site1The COM action with label site1 calculates the following quantities:
 Quantity   
 Type   
 Description  
site1
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tetrad3,tetrad2        # region of K1 ion that will serve as binding site reference
site2The COM action with label site2 calculates the following quantities:
 Quantity   
 Type   
 Description  
site2
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tetrad1,tetrad2        # region of K2 ion that will serve as binding site reference

KBULKThe GROUP action with label KBULK calculates the following quantities:
 Quantity   
 Type   
 Description  
KBULK
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe 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

check_site1The DISTANCE action with label check_site1 calculates the following quantities:
 Quantity   
 Type   
 Description  
check_site1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=K1,site1
check_site2The DISTANCE action with label check_site2 calculates the following quantities:
 Quantity   
 Type   
 Description  
check_site2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=K2,site2

WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=Klig AROUNDreference atoms=tetrad1,tetrad2,tetrad3

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

mindist1The DISTANCES action with label mindist1 calculates the following quantities:
 Quantity   
 Type   
 Description  
mindist1
vector
the DISTANCES between the each pair of atoms that were specified
mindist1_lowest
scalar
the smallest of the colvars: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K1 GROUPBCalculate 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
# PLUMED interprets the command:
# mindist1: DISTANCES GROUPA=K1 GROUPB=KBULK LOWEST
# as follows (Click the red comment above to revert to the short version of the input):
mindist1The DISTANCE action with label mindist1 calculates the following quantities:
 Quantity   
 Type   
 Description  
mindist1
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1517,35596 ATOMS2the pair of atom that we are calculating the distance between=1517,35598 ATOMS3the pair of atom that we are calculating the distance between=1517,35600 ATOMS4the pair of atom that we are calculating the distance between=1517,35602 ATOMS5the pair of atom that we are calculating the distance between=1517,35604     # Action input conctinues with 24 further ATOMSn keywords, 
mindist1_lowestThe LOWEST action with label mindist1_lowest calculates the following quantities:
 Quantity   
 Type   
 Description  
mindist1_lowest
scalar
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=mindist1
# --- End of included input --- repulsivewall1The LOWER_WALLS action with label repulsivewall1 calculates the following quantities:
 Quantity   
 Type   
 Description  
repulsivewall1.bias
scalar
the instantaneous value of the bias potential
repulsivewall1.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=mindist1.lowest ATthe positions of the wall=6.0 KAPPAthe 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

mindist2The DISTANCES action with label mindist2 calculates the following quantities:
 Quantity   
 Type   
 Description  
mindist2
vector
the DISTANCES between the each pair of atoms that were specified
mindist2_lowest
scalar
the smallest of the colvars: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K2 GROUPBCalculate 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
# PLUMED interprets the command:
# mindist2: DISTANCES GROUPA=K2 GROUPB=KBULK LOWEST
# as follows (Click the red comment above to revert to the short version of the input):
mindist2The DISTANCE action with label mindist2 calculates the following quantities:
 Quantity   
 Type   
 Description  
mindist2
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1519,35596 ATOMS2the pair of atom that we are calculating the distance between=1519,35598 ATOMS3the pair of atom that we are calculating the distance between=1519,35600 ATOMS4the pair of atom that we are calculating the distance between=1519,35602 ATOMS5the pair of atom that we are calculating the distance between=1519,35604     # Action input conctinues with 24 further ATOMSn keywords, 
mindist2_lowestThe LOWEST action with label mindist2_lowest calculates the following quantities:
 Quantity   
 Type   
 Description  
mindist2_lowest
scalar
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=mindist2
# --- End of included input --- repulsivewall2The LOWER_WALLS action with label repulsivewall2 calculates the following quantities:
 Quantity   
 Type   
 Description  
repulsivewall2.bias
scalar
the instantaneous value of the bias potential
repulsivewall2.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=mindist2.lowest ATthe positions of the wall=6.0 KAPPAthe 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

Klig_coordThe POSITION action with label Klig_coord calculates the following quantities:
 Quantity   
 Type   
 Description  
Klig_coord.x
scalar
the x-component of the atom position
Klig_coord.y
scalar
the y-component of the atom position
Klig_coord.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom. More details ATOMthe atom number=Klig NOPBC ignore the periodic boundary conditions when calculating distances
site1_coordThe POSITION action with label site1_coord calculates the following quantities:
 Quantity   
 Type   
 Description  
site1_coord.x
scalar
the x-component of the atom position
site1_coord.y
scalar
the y-component of the atom position
site1_coord.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom. More details ATOMthe atom number=site1 NOPBC ignore the periodic boundary conditions when calculating distances

# calculating the distance from site1 to Klig
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe 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
abs_xThe MATHEVAL action with label abs_x calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_x
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=Klig_coord.x,site1_coord.x FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abs_yThe MATHEVAL action with label abs_y calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_y
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=Klig_coord.y,site1_coord.y FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abs_zThe MATHEVAL action with label abs_z calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_z
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=Klig_coord.z,site1_coord.z FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Defining cylinder via descriptive coordinates
rhoThe MATHEVAL action with label rho calculates the following quantities:
 Quantity   
 Type   
 Description  
rho
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs_x,abs_y FUNCthe function you wish to evaluate=sqrt(x*x+y*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phiThe MATHEVAL action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs_x,abs_y FUNCthe function you wish to evaluate=atan2(y,x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-pi,pi

# restraining cylinder lateral size
cylrestr1The UPPER_WALLS action with label cylrestr1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cylrestr1.bias
scalar
the instantaneous value of the bias potential
cylrestr1.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=rho ATthe positions of the wall=7.0 KAPPAthe force constant for the wall=5000        # controls the maximum cylinder radius - 0.7 nm in this case

# restraining K1 from transpassing the cylinder heights
cylrestr2The LOWER_WALLS action with label cylrestr2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cylrestr2.bias
scalar
the instantaneous value of the bias potential
cylrestr2.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=d1.z ATthe positions of the wall=1.5  KAPPAthe 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
cylrestr3The UPPER_WALLS action with label cylrestr3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cylrestr3.bias
scalar
the instantaneous value of the bias potential
cylrestr3.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=d1.z ATthe positions of the wall=22.0 KAPPAthe 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

d1realThe DISTANCE action with label d1real calculates the following quantities:
 Quantity   
 Type   
 Description  
d1real
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=Klig,K1
d1real_xyzThe DISTANCE action with label d1real_xyz calculates the following quantities:
 Quantity   
 Type   
 Description  
d1real_xyz.x
scalar
the x-component of the vector connecting the two atoms
d1real_xyz.y
scalar
the y-component of the vector connecting the two atoms
d1real_xyz.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe 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

thetaxThe MATHEVAL action with label thetax calculates the following quantities:
 Quantity   
 Type   
 Description  
thetax
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs_x,d1real FUNCthe function you wish to evaluate=asin(x/y)*(180/pi) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
thetayThe MATHEVAL action with label thetay calculates the following quantities:
 Quantity   
 Type   
 Description  
thetay
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs_y,d1real FUNCthe function you wish to evaluate=asin(x/y)*(180/pi) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=d1.z,rho,phi SIGMAthe widths of the Gaussian hills=0.5,0.5,pi/8. HEIGHTthe heights of the Gaussian hills=1.0 PACEthe frequency for hill addition=500 FILE a file in which the list of added hills is stored=HILLS_CYL GRID_MINthe lower bounds for the grid=0.0,0.0,-pi GRID_MAXthe upper bounds for the grid=25.0,10.0,pi BIASFACTORuse 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] TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298

########################################
# Printing arguments
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_CYL
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.z,d1real,d1real_xyz.z FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=metad.* FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cylrestr1.*,cylrestr2.*,cylrestr3.* FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=mindist1.lowest,repulsivewall1.*,mindist2.lowest,repulsivewall2.* FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=abs_x,abs_y,abs_z FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rho,d1.z,phi FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=thetax,thetay FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=check_site1,check_site2 FILEthe 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
DUMPATOMSDump selected atoms on a file. More details STRIDE the frequency with which the atoms should be output=1000 FILEfile on which to output coordinates; extension is automatically detected=lig_coords.gro ATOMSthe atom indices whose positions you would like to print out=Klig

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