PLUMED-NEST

Project ID: plumID:19.017
Source: plumed_metad/metad_24ang.dat
Originally used with PLUMED version: 2.5
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

WHOLEMOLECULESThis 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=1-2593 ENTITY1the atoms that make up a molecule that you wish to align=2594-2605
The WHOLEMOLECULES action with label  calculates somethingFIT_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=../input/heavy_atoms.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

# Group definition
prot_noh: 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 NDX_FILEthe name of index file (gromacs syntax)=../input/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H
The GROUP action with label prot_noh calculates somethingsph: 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 NDX_FILEthe name of index file (gromacs syntax)=../input/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=sphere
The GROUP action with label sph calculates somethingbnz: 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 NDX_FILEthe name of index file (gromacs syntax)=../input/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=BNZ_noH

The GROUP action with label bnz calculates somethingWRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=bnz AROUNDreference atoms=sph

sph_center: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=sph
The COM action with label sph_center calculates somethingbnz_center: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=bnz

The COM action with label bnz_center calculates somethingsph_coord: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=sph_center NOPBC ignore the periodic boundary conditions when calculating distances
The POSITION action with label sph_coord calculates the following quantities:
 Quantity   
 Description  
sph_coord.x
the x-component of the atom position
sph_coord.y
the y-component of the atom position
sph_coord.z
the z-component of the atom positionbnz_coord: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=bnz_center NOPBC ignore the periodic boundary conditions when calculating distances

The POSITION action with label bnz_coord calculates the following quantities:
 Quantity   
 Description  
bnz_coord.x
the x-component of the atom position
bnz_coord.y
the y-component of the atom position
bnz_coord.z
the z-component of the atom positionabs_x: 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=bnz_coord.x,sph_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
The MATHEVAL action with label abs_x calculates the following quantities:
 Quantity   
 Description  
abs_x.value
an arbitrary functionabs_y: 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=bnz_coord.y,sph_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
The MATHEVAL action with label abs_y calculates the following quantities:
 Quantity   
 Description  
abs_y.value
an arbitrary functionabs_z: 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=bnz_coord.z,sph_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

The MATHEVAL action with label abs_z calculates the following quantities:
 Quantity   
 Description  
abs_z.value
an arbitrary functionrho: 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,abs_z FUNCthe function you wish to evaluate=sqrt(x*x+y*y+z*z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label rho calculates the following quantities:
 Quantity   
 Description  
rho.value
an arbitrary functiontheta: 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_z,rho FUNCthe function you wish to evaluate=acos(x/y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=0.,pi
The MATHEVAL action with label theta calculates the following quantities:
 Quantity   
 Description  
theta.value
an arbitrary functionphi: 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 potential of the sphere
The MATHEVAL action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
an arbitrary functionrestr: 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=2.4 KAPPAthe force constant for the wall=10000

# Coordination number
The UPPER_WALLS action with label restr calculates the following quantities:
 Quantity   
 Description  
restr.bias
the instantaneous value of the bias potential
restr.force2
the instantaneous value of the squared force due to this bias potentialc: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=bnz GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=prot_noh R_0The r_0 parameter of the switching function=0.45

# Metadynamics
The COORDINATION action with label c calculates the following quantities:
 Quantity   
 Description  
c.value
the value of the coordinationMETADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=rho,theta,phi
GRID_MINthe lower bounds for the grid=0,0.,-pi
GRID_MAXthe upper bounds for the grid=2.8,pi,pi
SIGMAthe widths of the Gaussian hills=0.1,pi/16.,pi/8.
HEIGHTthe heights of the Gaussian hills=1.2
PACEthe frequency for hill addition=500
BIASFACTORuse well tempered metadynamics and use this bias factor=20
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.
LABELa label for the action so that its output can be referenced in the input to other actions=metad
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD


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)PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rho 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=500
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=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=restr.* FILEthe name of the file on which to output these quantities=sphere_restraint.dat STRIDE the frequency with which the quantities of interest should be output=500
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=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rho,theta,phi FILEthe name of the file on which to output these quantities=rtp_coord.dat STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c FILEthe name of the file on which to output these quantities=all_coordination_45.dat STRIDE the frequency with which the quantities of interest should be output=500

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=500