Project ID: plumID:21.020
Source: hbr/smd/plumed.inp
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs
The UNITS action with label calculates somethingd1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,11 NOPBC ignore the periodic boundary conditions when calculating distances
d2The DISTANCE action with label d2 calculates the following quantities:| Quantity | Type | Description |
| d2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,1 NOPBC ignore the periodic boundary conditions when calculating distances
d3The DISTANCE action with label d3 calculates the following quantities:| Quantity | Type | Description |
| d3 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,2 NOPBC ignore the periodic boundary conditions when calculating distances
d4The DISTANCE action with label d4 calculates the following quantities:| Quantity | Type | Description |
| d4 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,2 NOPBC ignore the periodic boundary conditions when calculating distances
d5The DISTANCE action with label d5 calculates the following quantities:| Quantity | Type | Description |
| d5 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,1 NOPBC ignore the periodic boundary conditions when calculating distances
d6The DISTANCE action with label d6 calculates the following quantities:| Quantity | Type | Description |
| d6 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 NOPBC ignore the periodic boundary conditions when calculating distances
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:| Quantity | Type | Description |
| uwall.bias | scalar | the instantaneous value of the bias potential |
| uwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2,d3,d4,d5,d6 ATthe positions of the wall=3.0,3.0,3.0,3.0,3.0,3.0 KAPPAthe force constant for the wall=100,100,100,100,100,100
cvThe COMBINE action with label cv calculates the following quantities:| Quantity | Type | Description |
| cv | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5,d6 COEFFICIENTS the coefficients of the arguments in your function=0.661,-0.656,-0.328,0.011,-0.021,0.157 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=cv
STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0 AT0ATx is equal to the position of the restraint at time STEPx=-2.0 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=10000.0
STEP1This keyword appears multiple times as STEPx with x=0,1,2,=20000 AT1ATx is equal to the position of the restraint at time STEPx=1.0 KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=10000.0
LABELa label for the action so that its output can be referenced in the input to other actions=resThe MOVINGRESTRAINT action with label res calculates the following quantities:| Quantity | Type | Description |
| res.bias | scalar | the instantaneous value of the bias potential |
| res.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
| res.cv_cntr | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _cntr. These quantities give the instantaneous position of the center of the harmonic potential. This particular component measures this quantity for the input CV named cv |
| res.cv_work | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _work. These quantities tell the user how much work has been done by the potential in dragging the system along the various colvar axis. This particular component measures this quantity for the input CV named cv |
| res.cv_kappa | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _kappa. These quantities tell the user the time dependent value of kappa. This particular component measures this quantity for the input CV named cv |
| res.work | scalar | the total work performed changing this restraint |
... MOVINGRESTRAINT
MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=cv
STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0 AT0ATx is equal to the position of the restraint at time STEPx=-2.0 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=10000.0
STEP1This keyword appears multiple times as STEPx with x=0,1,2,=20000 AT1ATx is equal to the position of the restraint at time STEPx=1.0 KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=10000.0
LABELa label for the action so that its output can be referenced in the input to other actions=res
VERSE Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than the restraint or whether it is acting on both sides (B)=B
... MOVINGRESTRAINT
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=2000
PRINTPrint 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,cv,res.work STRIDE the frequency with which the quantities of interest should be output=2 FILEthe name of the file on which to output these quantities=colvar
