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=plumed
Enables 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
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=ref.pdb
RANDOM_EXCHANGES
Set random pattern for exchanges. More details
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1000

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file 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=plumed
Enables 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
#############################################################################################################

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

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

d1_lp1: ...
  
DISTANCE
Calculate the distance between a pair of atoms. More details
  
ATOMS
the pair of atom that we are calculating the distance between
=17,1311
...

The DISTANCE action with label d1_lp1 calculates a scalar quantityd2_lp1: ...
  
DISTANCE
Calculate the distance between a pair of atoms. More details
  
ATOMS
the pair of atom that we are calculating the distance between
=20,1312
...

The DISTANCE action with label d2_lp1 calculates a scalar quantityd3_lp1: ...
  
DISTANCE
Calculate the distance between a pair of atoms. More details
  
ATOMS
the pair of atom that we are calculating the distance between
=22,1315
...

The DISTANCE action with label d3_lp1 calculates a scalar quantitya1_lp1: ...
  
ANGLE
Calculate an angle. More details
  
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=17,19,1311
...

The ANGLE action with label a1_lp1 calculates a scalar quantitya2_lp1: ...
  
ANGLE
Calculate an angle. More details
  
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=1312,1313,20
...

The ANGLE action with label a2_lp1 calculates a scalar quantitya3_lp1: ...
  
ANGLE
Calculate an angle. More details
  
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=1315,1316,22
...

The ANGLE action with label a3_lp1 calculates a scalar quantitya4_lp1: ...
  
ANGLE
Calculate an angle. More details
  
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=12,20,1312
...

The ANGLE action with label a4_lp1 calculates a scalar quantitya5_lp1: ...
  
ANGLE
Calculate an angle. More details
  
ATOMS
the 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 a scalar quantityeRMSD_start: ...
  
ERMSD
Calculate eRMSD with respect to a reference structure. More details
  
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
,
@lcs-10
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
,
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
,
@lcs-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
,
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
,
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
,
@lcs-15
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. 
,
@lcs-16
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. 
,
@lcs-17
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information. 
,
@lcs-18
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. 
,
@lcs-19
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. 
,
@lcs-20
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. 
,
@lcs-21
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. 
,
@lcs-22
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. 
,
@lcs-23
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. 
,
@lcs-24
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. 
,
@lcs-25
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. 
,
@lcs-26
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. 
,
@lcs-27
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. 
,
@lcs-28
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 
,
@lcs-29
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information. 
,
@lcs-30
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. 
,
@lcs-31
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. 
,
@lcs-32
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. 
,
@lcs-33
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. 
,
@lcs-34
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. 
,
@lcs-35
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information. 
,
@lcs-36
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. Click here for more information. 
,
@lcs-37
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. 
,
@lcs-38
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. 
,
@lcs-39
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. 
,
@lcs-40
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. 
,
@lcs-41
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
  
REFERENCE
a 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 a scalar quantityu-wall_LPR: ...
  
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
  
ARG
the arguments on which the bias is acting
=d1_lp1,d2_lp1,d3_lp1 
AT
the positions of the wall
=0.30,0.30,0.30 
KAPPA
the 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
...

l-wall_aLPR: ...
  
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
  
ARG
the arguments on which the bias is acting
=a1_lp1,a2_lp1,a3_lp1,a4_lp1,a5_lp1 
AT
the positions of the wall
=2.75,2.75,2.75,2.75,2.75 
KAPPA
the 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
...

LBP-rest: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=1328,1329,1330,1334,1336,1338,1339,1340,1341,1342 
GROUPB
Calculate 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)
##################################################################################################

u-wall_eRMSD_start: ...
  
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
  
ARG
the arguments on which the bias is acting
=eRMSD_start 
AT
the positions of the wall
=0.6 
KAPPA
the force constant for the wall
=5000.0
...
 
l-wall_LBP-rest: ...
  
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
  
ARG
the arguments on which the bias is acting
=LBP-rest.lowest 
AT
the positions of the wall
=0.8 
KAPPA
the 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
...

u-wall_d-3: ...
  
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
  
ARG
the arguments on which the bias is acting
=d-3 
AT
the positions of the wall
=1.0 
KAPPA
the force constant for the wall
=50.0
...
 
####################################################################################################
# METADYNAMICS
####################################################################################################

metad: ...
  
METAD
Used to performed metadynamics on one or more collective variables. More details
  
ARG
the input for this action is the scalar output from one or more other actions
=d-3 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298.16 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=1.0 
SIGMA
the widths of the Gaussian hills
=0.02
  
GRID_MIN
the lower bounds for the grid
=0.01 
GRID_MAX
the 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 potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d-3,eRMSD_start,LBP-rest.lowest,metad.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
FILE
the name of the file on which to output these quantities
=COLVAR_SRP-motif_BzCN
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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 
FILE
the name of the file on which to output these quantities
=RESTR_BIAS_SRP-motif_BzCN