PLUMED-NEST

Project ID: plumID:19.001
Source: plumed-g3.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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
# choose units - by default PLUMED uses kj/mol, nm, and ps
# UNITS ENERGY=kcal/mol LENGTH=A
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=ref.pdb
The MOLINFO action with label  calculates somethingRANDOM_EXCHANGESSet random pattern for exchanges. More details
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

INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cv-s.dat
# The command:
# INCLUDE FILE=cv-s.dat
# ensures PLUMED loads the contents of the file called cv-s.dat
# The contents of this file are shown below (click the red comment to hide them).
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
# choose units - by default PLUMED uses kj/mol, nm, and ps
# UNITS ENERGY=kcal/mol LENGTH=A

#############################################################################################################
# ATOM SELECTIONS and CV definitions
#############################################################################################################

The INCLUDE action with label cv-s.dat calculates something  d-g3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=91,1339
  The DISTANCE action with label d-g3 calculates the following quantities:
 Quantity   
 Description  
d-g3.value
the DISTANCE between this pair of atomsd-u4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=121,1339
  The DISTANCE action with label d-u4 calculates the following quantities:
 Quantity   
 Description  
d-u4.value
the DISTANCE between this pair of atomsd-u5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=151,1339
  The DISTANCE action with label d-u5 calculates the following quantities:
 Quantity   
 Description  
d-u5.value
the DISTANCE between this pair of atomsd-u6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=181,1339
  The DISTANCE action with label d-u6 calculates the following quantities:
 Quantity   
 Description  
d-u6.value
the DISTANCE between this pair of atomsd-a7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=214,1339
  The DISTANCE action with label d-a7 calculates the following quantities:
 Quantity   
 Description  
d-a7.value
the DISTANCE between this pair of atomsd-c8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=245,1339
  The DISTANCE action with label d-c8 calculates the following quantities:
 Quantity   
 Description  
d-c8.value
the DISTANCE between this pair of atomsd-c9: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=276,1339
  The DISTANCE action with label d-c9 calculates the following quantities:
 Quantity   
 Description  
d-c9.value
the DISTANCE between this pair of atomsd-a10: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=309,1339
  The DISTANCE action with label d-a10 calculates the following quantities:
 Quantity   
 Description  
d-a10.value
the DISTANCE between this pair of atomsd-g11: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=343,1339
  The DISTANCE action with label d-g11 calculates the following quantities:
 Quantity   
 Description  
d-g11.value
the DISTANCE between this pair of atomsd-g12: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=377,1339
  The DISTANCE action with label d-g12 calculates the following quantities:
 Quantity   
 Description  
d-g12.value
the DISTANCE between this pair of atomsd-u13: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=407,1339
  The DISTANCE action with label d-u13 calculates the following quantities:
 Quantity   
 Description  
d-u13.value
the DISTANCE between this pair of atomsd-c14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=438,1339
  The DISTANCE action with label d-c14 calculates the following quantities:
 Quantity   
 Description  
d-c14.value
the DISTANCE between this pair of atomsd-a15: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=471,1339
  The DISTANCE action with label d-a15 calculates the following quantities:
 Quantity   
 Description  
d-a15.value
the DISTANCE between this pair of atomsd-g16: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=505,1339
  The DISTANCE action with label d-g16 calculates the following quantities:
 Quantity   
 Description  
d-g16.value
the DISTANCE between this pair of atomsd-g17: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=539,1339
  The DISTANCE action with label d-g17 calculates the following quantities:
 Quantity   
 Description  
d-g17.value
the DISTANCE between this pair of atomsd-u18: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=569,1339 
  The DISTANCE action with label d-u18 calculates the following quantities:
 Quantity   
 Description  
d-u18.value
the DISTANCE between this pair of atomsd-c19: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=600,1339
  The DISTANCE action with label d-c19 calculates the following quantities:
 Quantity   
 Description  
d-c19.value
the DISTANCE between this pair of atomsd-c20: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=631,1339
  The DISTANCE action with label d-c20 calculates the following quantities:
 Quantity   
 Description  
d-c20.value
the DISTANCE between this pair of atomsd-g21: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=665,1339
  The DISTANCE action with label d-g21 calculates the following quantities:
 Quantity   
 Description  
d-g21.value
the DISTANCE between this pair of atomsd-a22: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=698,1339
  The DISTANCE action with label d-a22 calculates the following quantities:
 Quantity   
 Description  
d-a22.value
the DISTANCE between this pair of atomsd-a23: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=731,1339
  The DISTANCE action with label d-a23 calculates the following quantities:
 Quantity   
 Description  
d-a23.value
the DISTANCE between this pair of atomsd-a24: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=764,1339
  The DISTANCE action with label d-a24 calculates the following quantities:
 Quantity   
 Description  
d-a24.value
the DISTANCE between this pair of atomsd-g25: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=798,1339
  The DISTANCE action with label d-g25 calculates the following quantities:
 Quantity   
 Description  
d-g25.value
the DISTANCE between this pair of atomsd-g26: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=832,1339
  The DISTANCE action with label d-g26 calculates the following quantities:
 Quantity   
 Description  
d-g26.value
the DISTANCE between this pair of atomsd-a27: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=865,1339
  The DISTANCE action with label d-a27 calculates the following quantities:
 Quantity   
 Description  
d-a27.value
the DISTANCE between this pair of atomsd-a28: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=898,1339
  The DISTANCE action with label d-a28 calculates the following quantities:
 Quantity   
 Description  
d-a28.value
the DISTANCE between this pair of atomsd-g29: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=932,1339
  The DISTANCE action with label d-g29 calculates the following quantities:
 Quantity   
 Description  
d-g29.value
the DISTANCE between this pair of atomsd-c30: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=963,1339
  The DISTANCE action with label d-c30 calculates the following quantities:
 Quantity   
 Description  
d-c30.value
the DISTANCE between this pair of atomsd-a31: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=996,1339
  The DISTANCE action with label d-a31 calculates the following quantities:
 Quantity   
 Description  
d-a31.value
the DISTANCE between this pair of atomsd-g32: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1030,1339
  The DISTANCE action with label d-g32 calculates the following quantities:
 Quantity   
 Description  
d-g32.value
the DISTANCE between this pair of atomsd-c33: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1061,1339
  The DISTANCE action with label d-c33 calculates the following quantities:
 Quantity   
 Description  
d-c33.value
the DISTANCE between this pair of atomsd-c34: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1092,1339
  The DISTANCE action with label d-c34 calculates the following quantities:
 Quantity   
 Description  
d-c34.value
the DISTANCE between this pair of atomsd-a35: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1125,1339
  The DISTANCE action with label d-a35 calculates the following quantities:
 Quantity   
 Description  
d-a35.value
the DISTANCE between this pair of atomsd-a36: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1158,1339
  The DISTANCE action with label d-a36 calculates the following quantities:
 Quantity   
 Description  
d-a36.value
the DISTANCE between this pair of atomsd-g37: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1192,1339
  The DISTANCE action with label d-g37 calculates the following quantities:
 Quantity   
 Description  
d-g37.value
the DISTANCE between this pair of atomsd-g38: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1226,1339

  The DISTANCE action with label d-g38 calculates the following quantities:
 Quantity   
 Description  
d-g38.value
the DISTANCE between this pair of atomsd-3: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-3 calculates the following quantities:
 Quantity   
 Description  
d-3.value
a linear compbinationd-4: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-u4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-4 calculates the following quantities:
 Quantity   
 Description  
d-4.value
a linear compbinationd-5: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-u5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-5 calculates the following quantities:
 Quantity   
 Description  
d-5.value
a linear compbinationd-6: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-u6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-6 calculates the following quantities:
 Quantity   
 Description  
d-6.value
a linear compbinationd-7: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a7 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-7 calculates the following quantities:
 Quantity   
 Description  
d-7.value
a linear compbinationd-8: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-c8 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-8 calculates the following quantities:
 Quantity   
 Description  
d-8.value
a linear compbinationd-9: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-c9 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-9 calculates the following quantities:
 Quantity   
 Description  
d-9.value
a linear compbinationd-10: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a10 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-10 calculates the following quantities:
 Quantity   
 Description  
d-10.value
a linear compbinationd-11: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g11 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-11 calculates the following quantities:
 Quantity   
 Description  
d-11.value
a linear compbinationd-12: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g12 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-12 calculates the following quantities:
 Quantity   
 Description  
d-12.value
a linear compbinationd-13: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-u13 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-13 calculates the following quantities:
 Quantity   
 Description  
d-13.value
a linear compbinationd-14: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-c14 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-14 calculates the following quantities:
 Quantity   
 Description  
d-14.value
a linear compbinationd-15: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a15 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-15 calculates the following quantities:
 Quantity   
 Description  
d-15.value
a linear compbinationd-16: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g16 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-16 calculates the following quantities:
 Quantity   
 Description  
d-16.value
a linear compbinationd-17: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g17 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-17 calculates the following quantities:
 Quantity   
 Description  
d-17.value
a linear compbinationd-18: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-u18 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-18 calculates the following quantities:
 Quantity   
 Description  
d-18.value
a linear compbinationd-19: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-c19 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-19 calculates the following quantities:
 Quantity   
 Description  
d-19.value
a linear compbinationd-20: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-c20 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-20 calculates the following quantities:
 Quantity   
 Description  
d-20.value
a linear compbinationd-21: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g21 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-21 calculates the following quantities:
 Quantity   
 Description  
d-21.value
a linear compbinationd-22: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a22 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-22 calculates the following quantities:
 Quantity   
 Description  
d-22.value
a linear compbinationd-23: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a23 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-23 calculates the following quantities:
 Quantity   
 Description  
d-23.value
a linear compbinationd-24: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a24 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-24 calculates the following quantities:
 Quantity   
 Description  
d-24.value
a linear compbinationd-25: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g25 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-25 calculates the following quantities:
 Quantity   
 Description  
d-25.value
a linear compbinationd-26: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g26 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-26 calculates the following quantities:
 Quantity   
 Description  
d-26.value
a linear compbinationd-27: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a27 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-27 calculates the following quantities:
 Quantity   
 Description  
d-27.value
a linear compbinationd-28: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a28 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-28 calculates the following quantities:
 Quantity   
 Description  
d-28.value
a linear compbinationd-29: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g29 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-29 calculates the following quantities:
 Quantity   
 Description  
d-29.value
a linear compbinationd-30: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-c30 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-30 calculates the following quantities:
 Quantity   
 Description  
d-30.value
a linear compbinationd-31: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a31 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-31 calculates the following quantities:
 Quantity   
 Description  
d-31.value
a linear compbinationd-32: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g32 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-32 calculates the following quantities:
 Quantity   
 Description  
d-32.value
a linear compbinationd-33: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-c33 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-33 calculates the following quantities:
 Quantity   
 Description  
d-33.value
a linear compbinationd-34: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-c34 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-34 calculates the following quantities:
 Quantity   
 Description  
d-34.value
a linear compbinationd-35: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a35 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-35 calculates the following quantities:
 Quantity   
 Description  
d-35.value
a linear compbinationd-36: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-a36 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-36 calculates the following quantities:
 Quantity   
 Description  
d-36.value
a linear compbinationd-37: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g37 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
  The COMBINE action with label d-37 calculates the following quantities:
 Quantity   
 Description  
d-37.value
a linear compbinationd-38: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d-g38 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# definition for ion restrain (by coordination for all ions from QM region)

The COMBINE action with label d-38 calculates the following quantities:
 Quantity   
 Description  
d-38.value
a linear compbinationd1_lp1: ...
  DISTANCECalculate the distance/s between pairs of atoms. More details
  ATOMSthe pair of atom that we are calculating the distance between=17,1311
...

The DISTANCE action with label d1_lp1 calculates the following quantities:
 Quantity   
 Description  
d1_lp1.value
the DISTANCE between this pair of atomsd2_lp1: ...
  DISTANCECalculate the distance/s between pairs of atoms. More details
  ATOMSthe pair of atom that we are calculating the distance between=20,1312
...

The DISTANCE action with label d2_lp1 calculates the following quantities:
 Quantity   
 Description  
d2_lp1.value
the DISTANCE between this pair of atomsd3_lp1: ...
  DISTANCECalculate the distance/s between pairs of atoms. More details
  ATOMSthe pair of atom that we are calculating the distance between=22,1315
...

The DISTANCE action with label d3_lp1 calculates the following quantities:
 Quantity   
 Description  
d3_lp1.value
the DISTANCE between this pair of atomsa1_lp1: ...
  ANGLECalculate one or multiple angle/s. More details
  ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=17,19,1311
...

The ANGLE action with label a1_lp1 calculates the following quantities:
 Quantity   
 Description  
a1_lp1.value
the ANGLE involving these atomsa2_lp1: ...
  ANGLECalculate one or multiple angle/s. More details
  ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1312,1313,20
...

The ANGLE action with label a2_lp1 calculates the following quantities:
 Quantity   
 Description  
a2_lp1.value
the ANGLE involving these atomsa3_lp1: ...
  ANGLECalculate one or multiple angle/s. More details
  ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1315,1316,22
...

The ANGLE action with label a3_lp1 calculates the following quantities:
 Quantity   
 Description  
a3_lp1.value
the ANGLE involving these atomsa4_lp1: ...
  ANGLECalculate one or multiple angle/s. More details
  ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=12,20,1312
...

The ANGLE action with label a4_lp1 calculates the following quantities:
 Quantity   
 Description  
a4_lp1.value
the ANGLE involving these atomsa5_lp1: ...
  ANGLECalculate one or multiple angle/s. More details
  ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1305,1312,20
...

# --- End of included input --- 
################################################################################################
# RESTRAINS, CONSTRAINS definition
################################################################################################

The ANGLE action with label a5_lp1 calculates the following quantities:
 Quantity   
 Description  
a5_lp1.value
the ANGLE involving these atomseRMSD_start: ...
  ERMSDCalculate eRMSD with respect to a reference structure. More details
  ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. ,@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. ,@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. ,@lcs-17an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information. ,@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. ,@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. ,@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. ,@lcs-21an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. ,@lcs-22an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. ,@lcs-23an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. ,@lcs-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. ,@lcs-25an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. ,@lcs-26an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. ,@lcs-27an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. ,@lcs-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. ,@lcs-29an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information. ,@lcs-30an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. ,@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. ,@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. ,@lcs-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. ,@lcs-34an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. ,@lcs-35an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information. ,@lcs-36an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. Click here for more information. ,@lcs-37an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. ,@lcs-38an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. ,@lcs-39an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. ,@lcs-40an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. ,@lcs-41an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=ref.pdb
...

The ERMSD action with label eRMSD_start calculates the following quantities:
 Quantity   
 Description  
eRMSD_start.value
the eRMSD between the instantaneous structure and the reference structure that was inputu-wall_LPR: ...
  UPPER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=d1_lp1,d2_lp1,d3_lp1 ATthe positions of the wall=0.30,0.30,0.30 KAPPAthe force constant for the wall=500.0,500.0,500.0 EXP the powers for the walls=2,2,2 EPS the values for s_i in the expression for a wall=1,1,1 OFFSET the offset for the start of the wall=0,0,0
...

The UPPER_WALLS action with label u-wall_LPR calculates the following quantities:
 Quantity   
 Description  
u-wall_LPR.bias
the instantaneous value of the bias potential
u-wall_LPR.force2
the instantaneous value of the squared force due to this bias potentiall-wall_aLPR: ...
  LOWER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=a1_lp1,a2_lp1,a3_lp1,a4_lp1,a5_lp1 ATthe positions of the wall=2.75,2.75,2.75,2.75,2.75 KAPPAthe force constant for the wall=100.0,100.0,100.0,100.0,100.0 EXP the powers for the walls=2,2,2,2,2 EPS the values for s_i in the expression for a wall=1,1,1,1,1 OFFSET the offset for the start of the wall=0,0,0,0,0
...

The LOWER_WALLS action with label l-wall_aLPR calculates the following quantities:
 Quantity   
 Description  
l-wall_aLPR.bias
the instantaneous value of the bias potential
l-wall_aLPR.force2
the instantaneous value of the squared force due to this bias potentialLBP-rest: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1328,1329,1330,1334,1336,1338,1339,1340,1341,1342 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1,3,6,8,9,11,12,14,16,17,20,21,22,23,25,27,29,1296,1297,1300,1302,1303,1305,1306,1308,1309,1310,1311,1312,1314,1315,1318,1319,1320,1322,1324,1326 LOWEST this flag allows you to recover the lowest of these variables

##################################################################################################
# WALLS (PES/FES restrictions)
##################################################################################################

The DISTANCES action with label LBP-rest calculates the following quantities:
 Quantity   
 Description  
LBP-rest.lowest
the smallest of the colvars
LBP-rest.value
the DISTANCES between the each pair of atoms that were specifiedu-wall_eRMSD_start: ...
  UPPER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=eRMSD_start ATthe positions of the wall=0.6 KAPPAthe force constant for the wall=5000.0
...
 
The UPPER_WALLS action with label u-wall_eRMSD_start calculates the following quantities:
 Quantity   
 Description  
u-wall_eRMSD_start.bias
the instantaneous value of the bias potential
u-wall_eRMSD_start.force2
the instantaneous value of the squared force due to this bias potentiall-wall_LBP-rest: ...
  LOWER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=LBP-rest.lowest ATthe positions of the wall=0.8 KAPPAthe force constant for the wall=5000.0 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 l-wall_LBP-rest calculates the following quantities:
 Quantity   
 Description  
l-wall_LBP-rest.bias
the instantaneous value of the bias potential
l-wall_LBP-rest.force2
the instantaneous value of the squared force due to this bias potentialu-wall_d-3: ...
  UPPER_WALLSDefines a wall for the value of one or more collective variables, More details
  ARGthe arguments on which the bias is acting=d-3 ATthe positions of the wall=1.0 KAPPAthe force constant for the wall=50.0
...
 
####################################################################################################
# METADYNAMICS
####################################################################################################

The UPPER_WALLS action with label u-wall_d-3 calculates the following quantities:
 Quantity   
 Description  
u-wall_d-3.bias
the instantaneous value of the bias potential
u-wall_d-3.force2
the instantaneous value of the squared force due to this bias potentialmetad: ...
  METADUsed to performed metadynamics on one or more collective variables. More details
  ARGthe labels of the scalars on which the bias will act=d-3 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298.16 BIASFACTORuse well tempered metadynamics and use this bias factor=5 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.0 SIGMAthe widths of the Gaussian hills=0.02
  GRID_MINthe lower bounds for the grid=0.01 GRID_MAXthe upper bounds for the grid=50.0 GRID_SPARSE use a sparse grid to store hills FILE a file in which the list of added hills is stored=HILLS_SRP-motif_BzCN
...

####################################################################################################
# OUTPUTS
####################################################################################################

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.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=d-3,eRMSD_start,LBP-rest.lowest,metad.bias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR_SRP-motif_BzCN
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=u-wall_d-3.bias,l-wall_LBP-rest.bias,u-wall_eRMSD_start.bias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=RESTR_BIAS_SRP-motif_BzCN