PLUMED-NEST

Project ID: plumID:25.029
Source: ./crys/2-eq2_crys.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

## second equilibrium. hrex after orbital pulling. close distances to AS.
#
#RESTART

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=1-3922      #3832 ENTITY1=3833-3922 # prot0 lig1
The WHOLEMOLECULES action with label  calculates somethingMOLINFOThis 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=cluster.pdb

DISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d0    ATOMSthe pair of atom that we are calculating the distance between=1911,3857                       # cat 160 SER OG vs UNK C19
The DISTANCE action with label d0 calculates the following quantities:
 Quantity   
 Description  
d0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d1    ATOMSthe pair of atom that we are calculating the distance between=3853,3885                         # ext UNK C17 vs C39
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=h0    ATOMSthe pair of atom that we are calculating the distance between=1915,3858                         # oxh 161 MET N vs O7
The DISTANCE action with label h0 calculates the following quantities:
 Quantity   
 Description  
h0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=h1    ATOMSthe pair of atom that we are calculating the distance between=797,3858                         # oxh 87 TYR N vs O7
The DISTANCE action with label h1 calculates the following quantities:
 Quantity   
 Description  
h1.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=s0    ATOMSthe pair of atom that we are calculating the distance between=1911,2991                    # cat 237 HIS NE2 vs cat 160 SER OG
The DISTANCE action with label s0 calculates the following quantities:
 Quantity   
 Description  
s0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=x0    ATOMSthe pair of atom that we are calculating the distance between=1911,1915                      # cat 160 SER OG vs oxh 161 MET N     # autohinibition
The DISTANCE action with label x0 calculates the following quantities:
 Quantity   
 Description  
x0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=x1    ATOMSthe pair of atom that we are calculating the distance between=1911,797                      # cat 160 SER OG vs oxh 87 TYR N     # autohinibition

The DISTANCE action with label x1 calculates the following quantities:
 Quantity   
 Description  
x1.value
the DISTANCE between this pair of atomsUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d0 ATthe positions of the wall=0.3 KAPPAthe force constant for the wall=5000 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 LABELa label for the action so that its output can be referenced in the input to other actions=d0_uwall        # 4A min distance from ser
The UPPER_WALLS action with label d0_uwall calculates the following quantities:
 Quantity   
 Description  
d0_uwall.bias
the instantaneous value of the bias potential
d0_uwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=h0 ATthe positions of the wall=0.3 KAPPAthe force constant for the wall=5000 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 LABELa label for the action so that its output can be referenced in the input to other actions=h0_uwall        # 4A min distance from hole
The UPPER_WALLS action with label h0_uwall calculates the following quantities:
 Quantity   
 Description  
h0_uwall.bias
the instantaneous value of the bias potential
h0_uwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=h1 ATthe positions of the wall=0.3 KAPPAthe force constant for the wall=5000 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 LABELa label for the action so that its output can be referenced in the input to other actions=h1_uwall        # 4A min distance from hole
The UPPER_WALLS action with label h1_uwall calculates the following quantities:
 Quantity   
 Description  
h1_uwall.bias
the instantaneous value of the bias potential
h1_uwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=s0 ATthe positions of the wall=0.3 KAPPAthe force constant for the wall=5000 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 LABELa label for the action so that its output can be referenced in the input to other actions=s0_uwall        # 4A min distance from hole

#LOWER_WALLS ARG=x0 AT=0.3 KAPPA=5000 EXP=2 EPS=1 OFFSET=0 LABEL=x0_uwall        # 4A max distance from hole
#LOWER_WALLS ARG=x1 AT=0.3 KAPPA=5000 EXP=2 EPS=1 OFFSET=0 LABEL=x1_uwall        # 4A max distance from hole

The UPPER_WALLS action with label s0_uwall calculates the following quantities:
 Quantity   
 Description  
s0_uwall.bias
the instantaneous value of the bias potential
s0_uwall.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=2550 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 LABELa label for the action so that its output can be referenced in the input to other actions=d1_lwall        # crystalline stretch

The LOWER_WALLS action with label d1_lwall calculates the following quantities:
 Quantity   
 Description  
d1_lwall.bias
the instantaneous value of the bias potential
d1_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=* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=colvar #print less