Project ID: plumID:23.028
Source: DeepMD_simulations/Unbiased/plumed.dat
Originally used with PLUMED version: 2.9
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
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
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=27,28,29,30,31,32,33,34,35,36,54,55,56,57,58,59,62,86,87,88,89,90,91,92,93,94,136,137,138,139,140,141,142,143,144,145,146,147,148,164,165,166,167,168,183,184,185,186,187,209,210,211,221,222,223,227,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,377,378,379,380,381,384,386,387,388,390,391,392
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=17,18,19,20,21,22,23,24,25,26,48,49,50,51,52,53,61,77,78,79,80,81,82,83,84,85,123,124,125,126,127,128,129,130,131,132,133,134,135,159,160,161,162,163,178,179,180,181,182,206,207,208,218,219,220,226,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,372,373,374,375,376,383,385,389
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=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,37,38,39,40,41,42,43,44,45,46,47,60,63,64,65,66,67,68,69,70,71,72,73,74,75,76,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,149,150,151,152,153,154,155,156,157,158,169,170,171,172,173,174,175,176,177,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,212,213,214,215,216,217,224,225,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,362,363,364,365,366,367,368,369,370,371,382
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
eneThe ENERGY action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
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,27 ATOMS2the pair of atom that we are calculating the distance between=ghosta,28 ATOMS3the pair of atom that we are calculating the distance between=ghosta,29 ATOMS4the pair of atom that we are calculating the distance between=ghosta,30 ATOMS5the pair of atom that we are calculating the distance between=ghosta,31
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,17 ATOMS2the pair of atom that we are calculating the distance between=ghosta,18 ATOMS3the pair of atom that we are calculating the distance between=ghosta,19 ATOMS4the pair of atom that we are calculating the distance between=ghosta,20 ATOMS5the pair of atom that we are calculating the distance between=ghosta,21
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
