Project ID: plumID:24.000
Source: scripts/LAMMPS/plumed_LAMMPS/plumed.driver.dat
Originally used with PLUMED version: 2.8.1
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
The UNITS action with label calculates somethingHThe GROUP action with label H calculates the following quantities:| Quantity | Type | Description |
| H | 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=1,2,3
NThe GROUP action with label N calculates the following quantities:| Quantity | Type | Description |
| N | 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=4,5,6
LiThe GROUP action with label Li calculates the following quantities:| Quantity | Type | Description |
| Li | 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=7,8,9
ghostaThe FIXEDATOM action with label ghosta calculates the following quantities:| Quantity | Type | Description |
| ghosta | atoms | virtual atom calculated by FIXEDATOM action |
: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,15
ghosta: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,15 SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
dis_GHThe ZDISTANCES action with label dis_GH calculates the following quantities:| Quantity | Type | Description |
| dis_GH_max | scalar | the maximum colvar |
: ZDISTANCESCalculate the z components of the vectors connecting one or many pairs of atoms. This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=ghosta GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MAXcalculate the maximum value={BETA=0.5}
# dis_GH: ZDISTANCES GROUPA=ghosta GROUPB=H MAX={BETA=0.5}
dis_GHThe DISTANCE action with label dis_GH calculates the following quantities:| Quantity | Type | Description |
| dis_GH.x | vector | the x-component of the vector connecting the two atoms |
| dis_GH.y | vector | the y-component of the vector connecting the two atoms |
| dis_GH.z | vector | the z-component of the vector connecting the two atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details COMPONENTS calculate the x, y and z components of the distance separately and store them as label ATOMS1the pair of atom that we are calculating the distance between=ghosta,1 ATOMS2the pair of atom that we are calculating the distance between=ghosta,2 ATOMS3the pair of atom that we are calculating the distance between=ghosta,3
dis_GH_me_maxThe CUSTOM action with label dis_GH_me_max calculates the following quantities:| Quantity | Type | Description |
| dis_GH_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=dis_GH.z FUNCthe function you wish to evaluate=exp(x/0.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dis_GH_mec_maxThe SUM action with label dis_GH_mec_max calculates the following quantities:| Quantity | Type | Description |
| dis_GH_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=dis_GH_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dis_GH_maxThe CUSTOM action with label dis_GH_max calculates the following quantities:| Quantity | Type | Description |
| dis_GH_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dis_GH_mec_max FUNCthe function you wish to evaluate=0.5*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities:| Quantity | Type | Description |
| uwall1.bias | scalar | the instantaneous value of the bias potential |
| uwall1.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=dis_GH.max ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2
dis_GNThe ZDISTANCES action with label dis_GN calculates the following quantities:| Quantity | Type | Description |
| dis_GN_max | scalar | the maximum colvar |
: ZDISTANCESCalculate the z components of the vectors connecting one or many pairs of atoms. This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=ghosta GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N MAXcalculate the maximum value={BETA=0.5}
# dis_GN: ZDISTANCES GROUPA=ghosta GROUPB=N MAX={BETA=0.5}
dis_GNThe DISTANCE action with label dis_GN calculates the following quantities:| Quantity | Type | Description |
| dis_GN.x | vector | the x-component of the vector connecting the two atoms |
| dis_GN.y | vector | the y-component of the vector connecting the two atoms |
| dis_GN.z | vector | the z-component of the vector connecting the two atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details COMPONENTS calculate the x, y and z components of the distance separately and store them as label ATOMS1the pair of atom that we are calculating the distance between=ghosta,4 ATOMS2the pair of atom that we are calculating the distance between=ghosta,5 ATOMS3the pair of atom that we are calculating the distance between=ghosta,6
dis_GN_me_maxThe CUSTOM action with label dis_GN_me_max calculates the following quantities:| Quantity | Type | Description |
| dis_GN_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=dis_GN.z FUNCthe function you wish to evaluate=exp(x/0.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dis_GN_mec_maxThe SUM action with label dis_GN_mec_max calculates the following quantities:| Quantity | Type | Description |
| dis_GN_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=dis_GN_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dis_GN_maxThe CUSTOM action with label dis_GN_max calculates the following quantities:| Quantity | Type | Description |
| dis_GN_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dis_GN_mec_max FUNCthe function you wish to evaluate=0.5*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities:| Quantity | Type | Description |
| uwall2.bias | scalar | the instantaneous value of the bias potential |
| uwall2.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=dis_GN.max ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1000
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=4000
