PLUMED-NEST

Project ID: plumID:24.028
Source: inputs/tip3p/16mer_elong/metadyn/plumed_metad.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

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=../conf.pdb
The MOLINFO action with label  calculates somethingmemb: 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 NDX_FILEthe name of index file (gromacs syntax)=../indices.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Phosphates
The GROUP action with label memb calculates somethingd_0: 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=33 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_0 calculates the following quantities:
 Quantity   
 Description  
d_0.lowest
the smallest of the colvars
d_0.value
the DISTANCES between the each pair of atoms that were specifiedd_1: 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=64 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_1 calculates the following quantities:
 Quantity   
 Description  
d_1.lowest
the smallest of the colvars
d_1.value
the DISTANCES between the each pair of atoms that were specifiedd_2: 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=98 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_2 calculates the following quantities:
 Quantity   
 Description  
d_2.lowest
the smallest of the colvars
d_2.value
the DISTANCES between the each pair of atoms that were specifiedd_3: 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=129 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_3 calculates the following quantities:
 Quantity   
 Description  
d_3.lowest
the smallest of the colvars
d_3.value
the DISTANCES between the each pair of atoms that were specifiedd_4: 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=163 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_4 calculates the following quantities:
 Quantity   
 Description  
d_4.lowest
the smallest of the colvars
d_4.value
the DISTANCES between the each pair of atoms that were specifiedd_5: 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=194 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_5 calculates the following quantities:
 Quantity   
 Description  
d_5.lowest
the smallest of the colvars
d_5.value
the DISTANCES between the each pair of atoms that were specifiedd_6: 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=225 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_6 calculates the following quantities:
 Quantity   
 Description  
d_6.lowest
the smallest of the colvars
d_6.value
the DISTANCES between the each pair of atoms that were specifiedd_7: 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=256 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_7 calculates the following quantities:
 Quantity   
 Description  
d_7.lowest
the smallest of the colvars
d_7.value
the DISTANCES between the each pair of atoms that were specifiedd_8: 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=287 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_8 calculates the following quantities:
 Quantity   
 Description  
d_8.lowest
the smallest of the colvars
d_8.value
the DISTANCES between the each pair of atoms that were specifiedd_9: 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=318 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_9 calculates the following quantities:
 Quantity   
 Description  
d_9.lowest
the smallest of the colvars
d_9.value
the DISTANCES between the each pair of atoms that were specifiedd_10: 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=352 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_10 calculates the following quantities:
 Quantity   
 Description  
d_10.lowest
the smallest of the colvars
d_10.value
the DISTANCES between the each pair of atoms that were specifiedd_11: 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=383 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_11 calculates the following quantities:
 Quantity   
 Description  
d_11.lowest
the smallest of the colvars
d_11.value
the DISTANCES between the each pair of atoms that were specifiedd_12: 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=417 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_12 calculates the following quantities:
 Quantity   
 Description  
d_12.lowest
the smallest of the colvars
d_12.value
the DISTANCES between the each pair of atoms that were specifiedd_13: 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=448 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_13 calculates the following quantities:
 Quantity   
 Description  
d_13.lowest
the smallest of the colvars
d_13.value
the DISTANCES between the each pair of atoms that were specifiedd_14: 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=482 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DISTANCES action with label d_14 calculates the following quantities:
 Quantity   
 Description  
d_14.lowest
the smallest of the colvars
d_14.value
the DISTANCES between the each pair of atoms that were specifiedsorted: SORTThis function can be used to sort colvars according to their magnitudes. More details ARGthe values input to this function=d_0.lowest,d_1.lowest,d_2.lowest,d_3.lowest,d_4.lowest,d_5.lowest,d_6.lowest,d_7.lowest,d_8.lowest,d_9.lowest,d_10.lowest,d_11.lowest,d_12.lowest,d_13.lowest,d_14.lowest
The SORT action with label sorted calculates the following quantities:
 Quantity   
 Description  
sorted.value
sortedmetad: METADUsed to performed metadynamics on one or more collective variables. More details ...

   ARGthe labels of the scalars on which the bias will act=sorted.1,sorted.15 SIGMAthe widths of the Gaussian hills=0.05,0.05 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=5 PACEthe frequency for hill addition=200 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=323
   GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=6.152625,6.152625
...


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialrg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=33,64,98,129,163,194,225,256,287,318,352,383,417,448,482
The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightslwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg  ATthe positions of the wall=1.8 KAPPAthe force constant for the wall=10000.0 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 lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=sorted.1,sorted.15,rg,lwall.bias,metad.bias FILEthe name of the file on which to output these quantities=METADYN STRIDE the frequency with which the quantities of interest should be output=10000