Project ID: plumID:19.058
Source: plumed_cylinder.dat
Originally used with PLUMED version: 2.5
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
COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3,25,39 LABELa label for the action so that its output can be referenced in the input to other actions=com1The COM action with label com1 calculates the following quantities:| Quantity | Type | Description |
| com1 | atoms | virtual atom calculated by COM action |
COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=49,69,81 LABELa label for the action so that its output can be referenced in the input to other actions=com2The COM action with label com2 calculates the following quantities:| Quantity | Type | Description |
| com2 | atoms | virtual atom calculated by COM action |
d1The INPLANEDISTANCES action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the INPLANEDISTANCE between each of the atoms specified using the GROUP keyword and atom A in the plane perpendicular to the vector connecting the atoms specified using VECTORSTART and VECTOREND |
| d1_min | scalar | the minimum colvar |
: INPLANEDISTANCESCalculate distances in the plane perpendicular to an axis This action is a shortcut. More details VECTORSTARTThe first atom position that is used to define the normal to the plane of interest=com1 VECTORENDThe second atom position that is used to defin the normal to the plane of interest=com2 GROUPcalculate distance for each distinct set of three atoms in the group=1-162 MINcalculate the minimum value={BETA=5}
# d1: INPLANEDISTANCES VECTORSTART=com1 VECTOREND=com2 GROUP=1-162 MIN={BETA=5}
d1_disThe DISTANCE action with label d1_dis calculates the following quantities:| Quantity | Type | Description |
| d1_dis | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=com1,1 ATOMS2the pair of atom that we are calculating the distance between=com1,2 ATOMS3the pair of atom that we are calculating the distance between=com1,3 ATOMS4the pair of atom that we are calculating the distance between=com1,4 ATOMS5the pair of atom that we are calculating the distance between=com1,5
d1_angThe ANGLE action with label d1_ang calculates the following quantities:| Quantity | Type | Description |
| d1_ang | vector | the ANGLE for each set of specified atoms |
: ANGLECalculate one or multiple angle/s. More details ATOMS1the list of atoms involved in this collective variable (either 3 or 4 atoms)=com2,com1,1 ATOMS2the list of atoms involved in this collective variable (either 3 or 4 atoms)=com2,com1,2 ATOMS3the list of atoms involved in this collective variable (either 3 or 4 atoms)=com2,com1,3 ATOMS4the list of atoms involved in this collective variable (either 3 or 4 atoms)=com2,com1,4 ATOMS5the list of atoms involved in this collective variable (either 3 or 4 atoms)=com2,com1,5
d1The CUSTOM action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=x*sin(y) ARGthe values input to this function=d1_dis,d1_ang
d1_me_minThe CUSTOM action with label d1_me_min calculates the following quantities:| Quantity | Type | Description |
| d1_me_min | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1 FUNCthe function you wish to evaluate=exp(5/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_mec_minThe SUM action with label d1_mec_min calculates the following quantities:| Quantity | Type | Description |
| d1_mec_min | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=d1_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_minThe CUSTOM action with label d1_min calculates the following quantities:| Quantity | Type | Description |
| d1_min | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_mec_min FUNCthe function you wish to evaluate=5/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
ARGthe labels of the scalars on which the bias will act=d1.min
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=0.5 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=0.0
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=0.5 KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=50000.0
LABELa label for the action so that its output can be referenced in the input to other actions=m1The MOVINGRESTRAINT action with label m1 calculates the following quantities:| Quantity | Type | Description |
| m1.bias | scalar | the instantaneous value of the bias potential |
| m1.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
| m1.d1_min_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 d1_min |
| m1.d1_min_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 d1_min |
| m1.d1_min_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 d1_min |
| m1.work | scalar | the total work performed changing this restraint |
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)=L
... MOVINGRESTRAINT
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.*,m1.* FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=10
The PRINT action with label calculates somethingFLUSHThis 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=10
