PLUMED-NEST

Project ID: plumID:25.011
Source: ChiralPerovskiteNucleation/plumed.dat
Originally used with PLUMED version: 2.9
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

RESTARTActivate restart. More details
The RESTART action with label  calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A  ENERGYthe units of energy=kcal/mol  timethe units of time=fs

MULTI_RMSDCalculate RMSD distances for different domains and combine them. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=Ligand1_2.pdb TYPE the manner in which RMSD alignment is performed=MULTI-SIMPLE LABELa label for the action so that its output can be referenced in the input to other actions=d1
The MULTI_RMSD action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the sum of the multiple RMSD distancesMULTI_RMSDCalculate RMSD distances for different domains and combine them. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=Ligand3_4.pdb TYPE the manner in which RMSD alignment is performed=MULTI-SIMPLE LABELa label for the action so that its output can be referenced in the input to other actions=d2

The MULTI_RMSD action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the sum of the multiple RMSD distancesc1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,5
The DISTANCE action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the DISTANCE between this pair of atomsc2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3
The DISTANCE action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.value
the DISTANCE between this pair of atomsc3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,4
The DISTANCE action with label c3 calculates the following quantities:
 Quantity   
 Description  
c3.value
the DISTANCE between this pair of atomsc4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,6
The DISTANCE action with label c4 calculates the following quantities:
 Quantity   
 Description  
c4.value
the DISTANCE between this pair of atomsc5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,2
The DISTANCE action with label c5 calculates the following quantities:
 Quantity   
 Description  
c5.value
the DISTANCE between this pair of atomsc6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,10
The DISTANCE action with label c6 calculates the following quantities:
 Quantity   
 Description  
c6.value
the DISTANCE between this pair of atomsc7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,8
The DISTANCE action with label c7 calculates the following quantities:
 Quantity   
 Description  
c7.value
the DISTANCE between this pair of atomsc8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,7
The DISTANCE action with label c8 calculates the following quantities:
 Quantity   
 Description  
c8.value
the DISTANCE between this pair of atomsc9: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,9


The DISTANCE action with label c9 calculates the following quantities:
 Quantity   
 Description  
c9.value
the DISTANCE between this pair of atomsdist_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=c1,c2,c3,c4,c5,c6,c7,c8,c9 VARthe names to give each of the arguments in the function=x,y,z,x1,y1,z1,x2,y2,z2 FUNCthe function you wish to evaluate=((x-3.2)^2+(y-3.2)^2+(z-3.2)^2+(x1-3.2)^2+(y1-3.2)^2+(z1-3.2)^2+(x2-3.2)^2+(y2-3.2)^2+(z2-3.2)^2)/8 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 


The MATHEVAL action with label dist_x calculates the following quantities:
 Quantity   
 Description  
dist_x.value
an arbitrary functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=dist_x
ATthe positions of the wall=0.25
KAPPAthe force constant for the wall=1000.0
LABELa label for the action so that its output can be referenced in the input to other actions=uwall-dist
... UPPER_WALLS

The UPPER_WALLS action with label uwall-dist calculates the following quantities:
 Quantity   
 Description  
uwall-dist.bias
the instantaneous value of the bias potential
uwall-dist.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ... 
ARGthe arguments on which the bias is acting=dist_x
ATthe positions of the wall=0.01
KAPPAthe force constant for the wall=1000.0
LABELa label for the action so that its output can be referenced in the input to other actions=lwall-sum_dist
... LOWER_WALLS


The LOWER_WALLS action with label lwall-sum_dist calculates the following quantities:
 Quantity   
 Description  
lwall-sum_dist.bias
the instantaneous value of the bias potential
lwall-sum_dist.force2
the instantaneous value of the squared force due to this bias potentialpb: PBMETADUsed to performed Parallel Bias metadynamics. More details ... 
ARGthe labels of the scalars on which the bias will act=d1,d2 SIGMAthe widths of the Gaussian hills=0.05,0.05 HEIGHTthe height of the Gaussian hills, one for all biases=0.4 
PACEthe frequency for hill addition, one for all biases=1 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=5 

FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_d1,HILLS_d2  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
WALKERS_Nnumber of walkers=9
WALKERS_IDwalker id=0
WALKERS_DIRshared directory with the hills files from all the walkers=../
WALKERS_RSTRIDEstride for reading hills files=1
... 

The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,dist_x,pb.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=COLVAR