PLUMED-NEST

Project ID: plumID:19.028
Source: Lysozyme/round3/plumed.3.dat
Originally used with PLUMED version: 2.3
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

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-2881


The WHOLEMOLECULES action with label  calculates somethinglig: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2870,2872,2874


The COM action with label lig calculates somethingd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1533
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1716
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2285
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2005
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1905
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2239 
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2424
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomsd8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2523

The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomshelix1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1416,1428,1452,1475,1501,1513,1533,1554,1566
The COM action with label helix1 calculates somethinghelix2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1964,1980,1994,2005,2028,2052,2071,2094,2111
The COM action with label helix2 calculates somethinghelix3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2176,2200,2212,2227,2239,2251,2271,2285,2308
The COM action with label helix3 calculates somethinghelix4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2535,2559,2583,2603,2626,2642,2658,2678,2702

The COM action with label helix4 calculates somethinghd12: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix1,helix2
The DISTANCE action with label hd12 calculates the following quantities:
 Quantity   
 Description  
hd12.value
the DISTANCE between this pair of atomshd23: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix2,helix3
The DISTANCE action with label hd23 calculates the following quantities:
 Quantity   
 Description  
hd23.value
the DISTANCE between this pair of atomshd34: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix3,helix4


The DISTANCE action with label hd34 calculates the following quantities:
 Quantity   
 Description  
hd34.value
the DISTANCE between this pair of atomsCOMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=rc1 ARGthe values input to this function=d1,d2,d3,d4,d5,d6,d7,d8,hd12,hd23,hd34  POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1,1,1,1,1,1,1 COEFFICIENTS the coefficients of the arguments in your function=-0.1065960692131182,-0.20375846578740134,0.2868449337215851,-0.3559391802958343,0.06772970987413295,0.6708182074106323,-0.24336006338372848,-0.40607423082695965,-0.10605373395450801,0.13541137840046852,0.17279650258546803 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO





The COMBINE action with label rc1 calculates the following quantities:
 Quantity   
 Description  
rc1.value
a linear compbinationEXTERNALCalculate a restraint that is defined on a grid that is read during start up More details ARGthe labels of the scalars on which the bias will act=rc1 FILEthe name of the file containing the external potential=static_bias.3.txt LABELa label for the action so that its output can be referenced in the input to other actions=external1


The EXTERNAL action with label external1 calculates the following quantities:
 Quantity   
 Description  
external1.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=d1,d2,d3,d4,d5,d6,d7,d8,hd12,hd23,hd34,rc1,external1.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=benzene_Lyso_T298_3