PLUMED-NEST-TEST-SITE

Click on the labels of the actions for more information on what each action computes

#plumed

#CN of ions

G25_N7: 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=788
The GROUP action with label G25_N7 calculates somethingC22_OH: 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=710
The GROUP action with label C22_OH calculates somethingU23_O2: 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=735
The GROUP action with label U23_O2 calculates somethingmg: 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=1066
The GROUP action with label mg calculates somethingna: 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=1067,1068,1090-1151

The GROUP action with label na calculates somethingna_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=710,1067
The DISTANCE action with label na_dist calculates the following quantities:
 Quantity   
 Description  
na_dist.value
the DISTANCE between this pair of atomsmg_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=788,1066

The DISTANCE action with label mg_dist calculates the following quantities:
 Quantity   
 Description  
mg_dist.value
the DISTANCE between this pair of atomsna_cn_1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=na GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C22_OH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label na_cn_1 calculates the following quantities:
 Quantity   
 Description  
na_cn_1.value
the value of the coordinationna_cn_2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=na GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=U23_O2 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label na_cn_2 calculates the following quantities:
 Quantity   
 Description  
na_cn_2.value
the value of the coordinationmg_cn: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=mg GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=G25_N7 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.45 NN=6 MM=10 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5

The COORDINATION action with label mg_cn calculates the following quantities:
 Quantity   
 Description  
mg_cn.value
the value of the coordinationPRINTPrint 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=1 FILEthe name of the file on which to output these quantities=COLVAR_driver FMT the format that should be used to output real numbers=%8.4f

The PRINT action with label  calculates somethingENDPLUMEDTerminate plumed input. More details