PLUMED-NEST

Project ID: plumID:21.039
Source: data/ala2-psi/1_opes_psi/plumed.dat
Originally used with PLUMED version: 2.8
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. 

####################################
#  >> Alanine Dipeptide <<
#  OPES simulation biasing PSI
####################################

# Define CVs
phiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17
eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details

# Define Descriptors
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=../plumed-descriptors.dat
# The command:
# INCLUDE FILE=../plumed-descriptors.dat
# ensures PLUMED loads the contents of the file called ../plumed-descriptors.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. 

####################################
#  >> Alanine Dipeptide <<
#  Aux. file - list of descriptors 
####################################

# Define descriptors
The INCLUDE action with label ../plumed-descriptors.dat calculates somethingd1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,5
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,6
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,7
d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,9
d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,11
d6The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,15
d7The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Type   
 Description  
d7
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,16
d8The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Type   
 Description  
d8
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,17
d9The DISTANCE action with label d9 calculates the following quantities:
 Quantity   
 Type   
 Description  
d9
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,19
d10The DISTANCE action with label d10 calculates the following quantities:
 Quantity   
 Type   
 Description  
d10
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,6
d11The DISTANCE action with label d11 calculates the following quantities:
 Quantity   
 Type   
 Description  
d11
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,7
d12The DISTANCE action with label d12 calculates the following quantities:
 Quantity   
 Type   
 Description  
d12
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,9
d13The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Type   
 Description  
d13
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,11
d14The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Type   
 Description  
d14
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,15
d15The DISTANCE action with label d15 calculates the following quantities:
 Quantity   
 Type   
 Description  
d15
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,16
d16The DISTANCE action with label d16 calculates the following quantities:
 Quantity   
 Type   
 Description  
d16
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,17
d17The DISTANCE action with label d17 calculates the following quantities:
 Quantity   
 Type   
 Description  
d17
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,19
d18The DISTANCE action with label d18 calculates the following quantities:
 Quantity   
 Type   
 Description  
d18
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,7
d19The DISTANCE action with label d19 calculates the following quantities:
 Quantity   
 Type   
 Description  
d19
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,9
d20The DISTANCE action with label d20 calculates the following quantities:
 Quantity   
 Type   
 Description  
d20
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,11
d21The DISTANCE action with label d21 calculates the following quantities:
 Quantity   
 Type   
 Description  
d21
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,15
d22The DISTANCE action with label d22 calculates the following quantities:
 Quantity   
 Type   
 Description  
d22
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,16
d23The DISTANCE action with label d23 calculates the following quantities:
 Quantity   
 Type   
 Description  
d23
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,17
d24The DISTANCE action with label d24 calculates the following quantities:
 Quantity   
 Type   
 Description  
d24
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,19
d25The DISTANCE action with label d25 calculates the following quantities:
 Quantity   
 Type   
 Description  
d25
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,9
d26The DISTANCE action with label d26 calculates the following quantities:
 Quantity   
 Type   
 Description  
d26
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,11
d27The DISTANCE action with label d27 calculates the following quantities:
 Quantity   
 Type   
 Description  
d27
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,15
d28The DISTANCE action with label d28 calculates the following quantities:
 Quantity   
 Type   
 Description  
d28
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,16
d29The DISTANCE action with label d29 calculates the following quantities:
 Quantity   
 Type   
 Description  
d29
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,17
d30The DISTANCE action with label d30 calculates the following quantities:
 Quantity   
 Type   
 Description  
d30
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,19
d31The DISTANCE action with label d31 calculates the following quantities:
 Quantity   
 Type   
 Description  
d31
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,11
d32The DISTANCE action with label d32 calculates the following quantities:
 Quantity   
 Type   
 Description  
d32
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,15
d33The DISTANCE action with label d33 calculates the following quantities:
 Quantity   
 Type   
 Description  
d33
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,16
d34The DISTANCE action with label d34 calculates the following quantities:
 Quantity   
 Type   
 Description  
d34
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,17
d35The DISTANCE action with label d35 calculates the following quantities:
 Quantity   
 Type   
 Description  
d35
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,19
d36The DISTANCE action with label d36 calculates the following quantities:
 Quantity   
 Type   
 Description  
d36
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,15
d37The DISTANCE action with label d37 calculates the following quantities:
 Quantity   
 Type   
 Description  
d37
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,16
d38The DISTANCE action with label d38 calculates the following quantities:
 Quantity   
 Type   
 Description  
d38
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,17
d39The DISTANCE action with label d39 calculates the following quantities:
 Quantity   
 Type   
 Description  
d39
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,19
d40The DISTANCE action with label d40 calculates the following quantities:
 Quantity   
 Type   
 Description  
d40
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,16
d41The DISTANCE action with label d41 calculates the following quantities:
 Quantity   
 Type   
 Description  
d41
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,17
d42The DISTANCE action with label d42 calculates the following quantities:
 Quantity   
 Type   
 Description  
d42
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,19
d43The DISTANCE action with label d43 calculates the following quantities:
 Quantity   
 Type   
 Description  
d43
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=16,17
d44The DISTANCE action with label d44 calculates the following quantities:
 Quantity   
 Type   
 Description  
d44
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=16,19
d45The DISTANCE action with label d45 calculates the following quantities:
 Quantity   
 Type   
 Description  
d45
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=17,19

ENDPLUMED
Terminate plumed input. More details

#ENDEXPANSION ../plumed-descriptors.dat

# Define Bias
#NODEFAULT opes
opes: OPES_METAD ARG=psi BARRIER=40 SIGMA=0.15 PACE=500 STATE_WFILE=STATE_PSI
#DEFAULT opes
opes: OPES_METAD ARG=psi BARRIER=40 SIGMA=0.15 PACE=500 STATE_WFILE=STATE_PSI  TEMP=-1 COMPRESSION_THRESHOLD=1 FILE=KERNELS
#ENDDEFAULT opes

PRINT FMT=%g STRIDE=2500 FILE=COLVAR ARG=*

ENDPLUMED
</pre>