Project ID: plumID:22.006
Source: mixed-gpu/metad.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
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=groups.txt
# INCLUDE FILE=groups.txt
The INCLUDE action with label groups.txt calculates somethingc1The GROUP action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5,6,7,9,20,21,22,24,40,41,42,44,60,61,62,64,70,71,72,74,80,81,82,84,95,99
c2The GROUP action with label c2 calculates the following quantities:| Quantity | Type | Description |
| c2 | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=104,105,106,108,119,120,121,123,139,140,141,143,159,160,161,163,169,170,171,173,179,180,181,183,194,198
c3The GROUP action with label c3 calculates the following quantities:| Quantity | Type | Description |
| c3 | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=203,204,205,207,225,226,227,229,245,246,247,249,265,266,267,269,275,276,277,279,285,286,287,289,307,311
c4The GROUP action with label c4 calculates the following quantities:| Quantity | Type | Description |
| c4 | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=316,317,318,320,338,339,340,342,358,359,360,362,378,379,380,382,388,389,390,392,398,399,400,402,420,424
# --- End of included input ---
c1comThe COM action with label c1com calculates the following quantities:| Quantity | Type | Description |
| c1com | 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=c1
c2comThe COM action with label c2com calculates the following quantities:| Quantity | Type | Description |
| c2com | 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=c2
c3comThe COM action with label c3com calculates the following quantities:| Quantity | Type | Description |
| c3com | 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=c3
c4comThe COM action with label c4com calculates the following quantities:| Quantity | Type | Description |
| c4com | 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=c4
distThe DISTANCES action with label dist calculates the following quantities:| Quantity | Type | Description |
| dist | vector | the DISTANCES between the each pair of atoms that were specified |
| dist_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPCalculate the distance between each distinct pair of atoms in the group=c1com,c2com,c3com,c4com MEAN calculate the mean of all the quantities
# dist: DISTANCES GROUP=c1com,c2com,c3com,c4com MEAN
distThe DISTANCE action with label dist calculates the following quantities:| Quantity | Type | Description |
| dist | 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=c2com,c1com ATOMS2the pair of atom that we are calculating the distance between=c3com,c1com ATOMS3the pair of atom that we are calculating the distance between=c3com,c2com ATOMS4the pair of atom that we are calculating the distance between=c4com,c1com ATOMS5the pair of atom that we are calculating the distance between=c4com,c2com
dist_meanThe MEAN action with label dist_mean calculates the following quantities:| Quantity | Type | Description |
| dist_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dist PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
rg1The GYRATION action with label rg1 calculates the following quantities:| Quantity | Type | Description |
| rg1 | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c1
rg2The GYRATION action with label rg2 calculates the following quantities:| Quantity | Type | Description |
| rg2 | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c2
rg3The GYRATION action with label rg3 calculates the following quantities:| Quantity | Type | Description |
| rg3 | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c3
rg4The GYRATION action with label rg4 calculates the following quantities:| Quantity | Type | Description |
| rg4 | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c4
rgThe COMBINE action with label rg calculates the following quantities:| Quantity | Type | Description |
| rg | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=rg1,rg2,rg3,rg4 NORMALIZE normalize all the coefficients so that in total they are equal to one PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dist.mean,rg 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
The PRINT action with label calculates somethingMETADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=dist.mean,rg PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=5 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 SIGMAthe widths of the Gaussian hills=0.05,0.01
GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=5,1.5 GRID_BINthe number of bins for the grid=500,500 HEIGHTthe heights of the Gaussian hills=5
... METAD
