PLUMED-NEST-TEST-SITE

Project ID: plumID:24.008
Source: Uracil/Volume_MetaD_Input/plumed_run.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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../Structure/yCD_uracil.pdb
The MOLINFO 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=1-2423 ENTITY1the atoms that make up a molecule that you wish to align=2424-4846 ENTITY2the atoms that make up a molecule that you wish to align=4847-4858 ENTITY3the atoms that make up a molecule that you wish to align=4859-4870
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=../Structure/heavy_atoms.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

# Group definitions
sphThe GROUP action with label sph calculates the following quantities:
 Quantity   
 Type   
 Description  
sph
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 NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=ChainA-H_ZN-ChainA 
urlThe GROUP action with label url calculates the following quantities:
 Quantity   
 Type   
 Description  
url
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 NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=UR1_noH
ligThe GROUP action with label lig calculates the following quantities:
 Quantity   
 Type   
 Description  
lig
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 NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=UR1
refThe GROUP action with label ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ref
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 NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H_ZN
# Group sys 
sysThe GROUP action with label sys calculates the following quantities:
 Quantity   
 Type   
 Description  
sys
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 NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein_ZN_UR1_UR2


WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=lig AROUNDreference atoms=sph

# Now we need to remake whole molecules
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=1-2423 ENTITY1the atoms that make up a molecule that you wish to align=2424-4846 ENTITY2the atoms that make up a molecule that you wish to align=4847-4858 ENTITY3the atoms that make up a molecule that you wish to align=4859-4870 ENTITY4the atoms that make up a molecule that you wish to align=4957-4959 ENTITY5the atoms that make up a molecule that you wish to align=4960-4962
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=../Structure/chainA_template.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

# Fix
fixThe FIXEDATOM action with label fix calculates the following quantities:
 Quantity   
 Type   
 Description  
fix
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=-1.101616,-0.678271,0.017793
fix: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=-1.101616,-0.678271,0.017793  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0

sph_centerThe COM action with label sph_center calculates the following quantities:
 Quantity   
 Type   
 Description  
sph_center
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=sph
url_centerThe COM action with label url_center calculates the following quantities:
 Quantity   
 Type   
 Description  
url_center
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=url

disThe DISTANCE action with label dis calculates the following quantities:
 Quantity   
 Type   
 Description  
dis
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=sph_center,fix


# Define volume based CVs 
absThe DISTANCE action with label abs calculates the following quantities:
 Quantity   
 Type   
 Description  
abs.x
scalar
the x-component of the vector connecting the two atoms
abs.y
scalar
the y-component of the vector connecting the two atoms
abs.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=url_center,sph_center COMPONENTS calculate the x, y and z components of the distance separately and store them as label
rhoThe DISTANCE action with label rho calculates the following quantities:
 Quantity   
 Type   
 Description  
rho
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=url_center,sph_center
rel_xThe MATHEVAL action with label rel_x calculates the following quantities:
 Quantity   
 Type   
 Description  
rel_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=abs.z,abs.y FUNCthe function you wish to evaluate=(x-y)/sqrt(2) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
rel_yThe MATHEVAL action with label rel_y calculates the following quantities:
 Quantity   
 Type   
 Description  
rel_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=abs.x FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
rel_zThe MATHEVAL action with label rel_z calculates the following quantities:
 Quantity   
 Type   
 Description  
rel_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=abs.z,abs.y FUNCthe function you wish to evaluate=(x+y)/sqrt(2) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

thetaThe MATHEVAL action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
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=rel_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
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=rel_x,rel_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

rmsdThe RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../Structure/heavy_atoms_UR2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../Structure/heavy_atoms_UR2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

# Restraining potential of the sphere
restrThe UPPER_WALLS action with label restr calculates the following quantities:
 Quantity   
 Type   
 Description  
restr.bias
scalar
the instantaneous value of the bias potential
restr.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=2.8 KAPPAthe force constant for the wall=200
restr2The UPPER_WALLS action with label restr2 calculates the following quantities:
 Quantity   
 Type   
 Description  
restr2.bias
scalar
the instantaneous value of the bias potential
restr2.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=rmsd ATthe positions of the wall=0.1 KAPPAthe force constant for the wall=200

# Coordination number
cThe COORDINATION action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=url GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=sph R_0The r_0 parameter of the switching function=0.45
c: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=url GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=sph R_0The r_0 parameter of the switching function=0.45  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0

# Metadynamics
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. 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=5,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=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).
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. 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=5,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]
 FILE a file in which the list of added hills is stored=HILLS
... METAD

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rho,dis 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,rel_x,rel_y,rel_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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=restr2.* FILEthe name of the file on which to output these quantities=rmsd_restraint.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