Project ID: plumID:19.058
Source: plumed_sphere.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
RESTARTActivate restart. More details
The RESTART action with label calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-216 LABELa label for the action so that its output can be referenced in the input to other actions=comThe COM action with label com calculates the following quantities:| Quantity | Type | Description |
| com | atoms | virtual atom calculated by COM action |
DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=com GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-216 MINcalculate the minimum value={BETA=10} MAXcalculate the maximum value={BETA=.001} LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCES action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the DISTANCES between the each pair of atoms that were specified |
| d1_min | scalar | the minimum colvar |
| d1_max | scalar | the maximum colvar |
# DISTANCES GROUPA=com GROUPB=1-216 MIN={BETA=10} MAX={BETA=.001} LABEL=d1
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | 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=com,1 ATOMS2the pair of atom that we are calculating the distance between=com,2 ATOMS3the pair of atom that we are calculating the distance between=com,3 ATOMS4the pair of atom that we are calculating the distance between=com,4 ATOMS5the pair of atom that we are calculating the distance between=com,5
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(10/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=10/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_me_maxThe CUSTOM action with label d1_me_max calculates the following quantities:| Quantity | Type | Description |
| d1_me_max | 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(x/.001) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_mec_maxThe SUM action with label d1_mec_max calculates the following quantities:| Quantity | Type | Description |
| d1_mec_max | 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_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1_maxThe CUSTOM action with label d1_max calculates the following quantities:| Quantity | Type | Description |
| d1_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1_mec_max FUNCthe function you wish to evaluate=.001*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
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=10
