PLUMED-NEST

Project ID: plumID:23.025
Source: repulsive/3ibk/terra_repulsive.dat
Originally used with PLUMED version: 2.7
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 # modify the default length unit (nm) to Angstrom

# TERRA GQ
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# PDB NUMBERING MUST BE USED HERE
# K1 = 1517 (pdb numbering)
# K2 = 1519 (pdb numbering)
# Kbulk = 35596-35655 (remove drude particles from list!) (pdb numbering)
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# Defining groups and lower_walls
K1The GROUP action with label K1 calculates the following quantities:
 Quantity   
 Type   
 Description  
K1
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1517
K2The GROUP action with label K2 calculates the following quantities:
 Quantity   
 Type   
 Description  
K2
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1519
KBULKThe GROUP action with label KBULK calculates the following quantities:
 Quantity   
 Type   
 Description  
KBULK
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=35596,35598,35600,35602,35604,35606,35608,35610,35612,35614,35616,35618,35620,35622,35624,35626,35628,35630,35632,35634,35636,35638,35640,35642,35644,35646,35648,35650,35652,35654


d1The DISTANCES action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
vector
the DISTANCES between the each pair of atoms that were specified
d1_lowest
scalar
the smallest of the colvars: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=KBULK LOWEST this flag allows you to recover the lowest of these variables
# PLUMED interprets the command:
# d1: DISTANCES GROUPA=K1 GROUPB=KBULK LOWEST
# as follows (Click the red comment above to revert to the short version of the input):
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1517,35596 ATOMS2the pair of atom that we are calculating the distance between=1517,35598 ATOMS3the pair of atom that we are calculating the distance between=1517,35600 ATOMS4the pair of atom that we are calculating the distance between=1517,35602 ATOMS5the pair of atom that we are calculating the distance between=1517,35604     # Action input conctinues with 25 further ATOMSn keywords, 
d1_lowestThe LOWEST action with label d1_lowest calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_lowest
scalar
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d1
# --- End of included input --- d2The DISTANCES action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
vector
the DISTANCES between the each pair of atoms that were specified
d2_lowest
scalar
the smallest of the colvars: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=KBULK LOWEST this flag allows you to recover the lowest of these variables
# PLUMED interprets the command:
# d2: DISTANCES GROUPA=K2 GROUPB=KBULK LOWEST
# as follows (Click the red comment above to revert to the short version of the input):
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1519,35596 ATOMS2the pair of atom that we are calculating the distance between=1519,35598 ATOMS3the pair of atom that we are calculating the distance between=1519,35600 ATOMS4the pair of atom that we are calculating the distance between=1519,35602 ATOMS5the pair of atom that we are calculating the distance between=1519,35604     # Action input conctinues with 25 further ATOMSn keywords, 
d2_lowestThe LOWEST action with label d2_lowest calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_lowest
scalar
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d2
# --- End of included input --- d3The DISTANCES action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
vector
the DISTANCES between the each pair of atoms that were specified
d3_lowest
scalar
the smallest of the colvars: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K2 LOWEST this flag allows you to recover the lowest of these variables
# PLUMED interprets the command:
# d3: DISTANCES GROUPA=K1 GROUPB=K2 LOWEST
# as follows (Click the red comment above to revert to the short version of the input):
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1517,1519
d3_lowestThe LOWEST action with label d3_lowest calculates the following quantities:
 Quantity   
 Type   
 Description  
d3_lowest
scalar
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d3
# --- End of included input --- 
lwall1The LOWER_WALLS action with label lwall1 calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall1.bias
scalar
the instantaneous value of the bias potential
lwall1.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.lowest ATthe positions of the wall=5.5 KAPPAthe force constant for the wall=2000.0 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
lwall2The LOWER_WALLS action with label lwall2 calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall2.bias
scalar
the instantaneous value of the bias potential
lwall2.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d2.lowest ATthe positions of the wall=5.5 KAPPAthe force constant for the wall=2000.0 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
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PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=d1.lowest,d2.lowest,d3.lowest FILEthe name of the file on which to output these quantities=mindist.dat