Project ID: plumID:24.028
Source: inputs/tip3p/16mer_elong/metadyn/plumed_metad.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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../conf.pdb
The MOLINFO action with label calculates somethingmembThe GROUP action with label memb calculates the following quantities:| Quantity | Type | Description |
| memb | 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 NDX_FILEthe name of index file (gromacs syntax)=../indices.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Phosphates
d_0The DISTANCES action with label d_0 calculates the following quantities:| Quantity | Type | Description |
| d_0 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_0_lowest | scalar | the smallest of the colvars |
: 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=33 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_0: DISTANCES GROUPA=33 GROUPB=memb LOWEST LOWMEM
d_0The DISTANCE action with label d_0 calculates the following quantities:| Quantity | Type | Description |
| d_0 | 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=33,572 ATOMS2the pair of atom that we are calculating the distance between=33,702 ATOMS3the pair of atom that we are calculating the distance between=33,832 ATOMS4the pair of atom that we are calculating the distance between=33,962 ATOMS5the pair of atom that we are calculating the distance between=33,1092
d_0_lowestThe LOWEST action with label d_0_lowest calculates the following quantities:| Quantity | Type | Description |
| d_0_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_0
# --- End of included input --- d_1The DISTANCES action with label d_1 calculates the following quantities:| Quantity | Type | Description |
| d_1 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_1_lowest | scalar | the smallest of the colvars |
: 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=64 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_1: DISTANCES GROUPA=64 GROUPB=memb LOWEST LOWMEM
d_1The DISTANCE action with label d_1 calculates the following quantities:| Quantity | Type | Description |
| d_1 | 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=64,572 ATOMS2the pair of atom that we are calculating the distance between=64,702 ATOMS3the pair of atom that we are calculating the distance between=64,832 ATOMS4the pair of atom that we are calculating the distance between=64,962 ATOMS5the pair of atom that we are calculating the distance between=64,1092
d_1_lowestThe LOWEST action with label d_1_lowest calculates the following quantities:| Quantity | Type | Description |
| d_1_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_1
# --- End of included input --- d_2The DISTANCES action with label d_2 calculates the following quantities:| Quantity | Type | Description |
| d_2 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_2_lowest | scalar | the smallest of the colvars |
: 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=98 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_2: DISTANCES GROUPA=98 GROUPB=memb LOWEST LOWMEM
d_2The DISTANCE action with label d_2 calculates the following quantities:| Quantity | Type | Description |
| d_2 | 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=98,572 ATOMS2the pair of atom that we are calculating the distance between=98,702 ATOMS3the pair of atom that we are calculating the distance between=98,832 ATOMS4the pair of atom that we are calculating the distance between=98,962 ATOMS5the pair of atom that we are calculating the distance between=98,1092
d_2_lowestThe LOWEST action with label d_2_lowest calculates the following quantities:| Quantity | Type | Description |
| d_2_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_2
# --- End of included input --- d_3The DISTANCES action with label d_3 calculates the following quantities:| Quantity | Type | Description |
| d_3 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_3_lowest | scalar | the smallest of the colvars |
: 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=129 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_3: DISTANCES GROUPA=129 GROUPB=memb LOWEST LOWMEM
d_3The DISTANCE action with label d_3 calculates the following quantities:| Quantity | Type | Description |
| d_3 | 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=129,572 ATOMS2the pair of atom that we are calculating the distance between=129,702 ATOMS3the pair of atom that we are calculating the distance between=129,832 ATOMS4the pair of atom that we are calculating the distance between=129,962 ATOMS5the pair of atom that we are calculating the distance between=129,1092
d_3_lowestThe LOWEST action with label d_3_lowest calculates the following quantities:| Quantity | Type | Description |
| d_3_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_3
# --- End of included input --- d_4The DISTANCES action with label d_4 calculates the following quantities:| Quantity | Type | Description |
| d_4 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_4_lowest | scalar | the smallest of the colvars |
: 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=163 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_4: DISTANCES GROUPA=163 GROUPB=memb LOWEST LOWMEM
d_4The DISTANCE action with label d_4 calculates the following quantities:| Quantity | Type | Description |
| d_4 | 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=163,572 ATOMS2the pair of atom that we are calculating the distance between=163,702 ATOMS3the pair of atom that we are calculating the distance between=163,832 ATOMS4the pair of atom that we are calculating the distance between=163,962 ATOMS5the pair of atom that we are calculating the distance between=163,1092
d_4_lowestThe LOWEST action with label d_4_lowest calculates the following quantities:| Quantity | Type | Description |
| d_4_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_4
# --- End of included input --- d_5The DISTANCES action with label d_5 calculates the following quantities:| Quantity | Type | Description |
| d_5 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_5_lowest | scalar | the smallest of the colvars |
: 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=194 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_5: DISTANCES GROUPA=194 GROUPB=memb LOWEST LOWMEM
d_5The DISTANCE action with label d_5 calculates the following quantities:| Quantity | Type | Description |
| d_5 | 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=194,572 ATOMS2the pair of atom that we are calculating the distance between=194,702 ATOMS3the pair of atom that we are calculating the distance between=194,832 ATOMS4the pair of atom that we are calculating the distance between=194,962 ATOMS5the pair of atom that we are calculating the distance between=194,1092
d_5_lowestThe LOWEST action with label d_5_lowest calculates the following quantities:| Quantity | Type | Description |
| d_5_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_5
# --- End of included input --- d_6The DISTANCES action with label d_6 calculates the following quantities:| Quantity | Type | Description |
| d_6 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_6_lowest | scalar | the smallest of the colvars |
: 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=225 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_6: DISTANCES GROUPA=225 GROUPB=memb LOWEST LOWMEM
d_6The DISTANCE action with label d_6 calculates the following quantities:| Quantity | Type | Description |
| d_6 | 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=225,572 ATOMS2the pair of atom that we are calculating the distance between=225,702 ATOMS3the pair of atom that we are calculating the distance between=225,832 ATOMS4the pair of atom that we are calculating the distance between=225,962 ATOMS5the pair of atom that we are calculating the distance between=225,1092
d_6_lowestThe LOWEST action with label d_6_lowest calculates the following quantities:| Quantity | Type | Description |
| d_6_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_6
# --- End of included input --- d_7The DISTANCES action with label d_7 calculates the following quantities:| Quantity | Type | Description |
| d_7 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_7_lowest | scalar | the smallest of the colvars |
: 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=256 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_7: DISTANCES GROUPA=256 GROUPB=memb LOWEST LOWMEM
d_7The DISTANCE action with label d_7 calculates the following quantities:| Quantity | Type | Description |
| d_7 | 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=256,572 ATOMS2the pair of atom that we are calculating the distance between=256,702 ATOMS3the pair of atom that we are calculating the distance between=256,832 ATOMS4the pair of atom that we are calculating the distance between=256,962 ATOMS5the pair of atom that we are calculating the distance between=256,1092
d_7_lowestThe LOWEST action with label d_7_lowest calculates the following quantities:| Quantity | Type | Description |
| d_7_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_7
# --- End of included input --- d_8The DISTANCES action with label d_8 calculates the following quantities:| Quantity | Type | Description |
| d_8 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_8_lowest | scalar | the smallest of the colvars |
: 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=287 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_8: DISTANCES GROUPA=287 GROUPB=memb LOWEST LOWMEM
d_8The DISTANCE action with label d_8 calculates the following quantities:| Quantity | Type | Description |
| d_8 | 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=287,572 ATOMS2the pair of atom that we are calculating the distance between=287,702 ATOMS3the pair of atom that we are calculating the distance between=287,832 ATOMS4the pair of atom that we are calculating the distance between=287,962 ATOMS5the pair of atom that we are calculating the distance between=287,1092
d_8_lowestThe LOWEST action with label d_8_lowest calculates the following quantities:| Quantity | Type | Description |
| d_8_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_8
# --- End of included input --- d_9The DISTANCES action with label d_9 calculates the following quantities:| Quantity | Type | Description |
| d_9 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_9_lowest | scalar | the smallest of the colvars |
: 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=318 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_9: DISTANCES GROUPA=318 GROUPB=memb LOWEST LOWMEM
d_9The DISTANCE action with label d_9 calculates the following quantities:| Quantity | Type | Description |
| d_9 | 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=318,572 ATOMS2the pair of atom that we are calculating the distance between=318,702 ATOMS3the pair of atom that we are calculating the distance between=318,832 ATOMS4the pair of atom that we are calculating the distance between=318,962 ATOMS5the pair of atom that we are calculating the distance between=318,1092
d_9_lowestThe LOWEST action with label d_9_lowest calculates the following quantities:| Quantity | Type | Description |
| d_9_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_9
# --- End of included input --- d_10The DISTANCES action with label d_10 calculates the following quantities:| Quantity | Type | Description |
| d_10 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_10_lowest | scalar | the smallest of the colvars |
: 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=352 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_10: DISTANCES GROUPA=352 GROUPB=memb LOWEST LOWMEM
d_10The DISTANCE action with label d_10 calculates the following quantities:| Quantity | Type | Description |
| d_10 | 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=352,572 ATOMS2the pair of atom that we are calculating the distance between=352,702 ATOMS3the pair of atom that we are calculating the distance between=352,832 ATOMS4the pair of atom that we are calculating the distance between=352,962 ATOMS5the pair of atom that we are calculating the distance between=352,1092
d_10_lowestThe LOWEST action with label d_10_lowest calculates the following quantities:| Quantity | Type | Description |
| d_10_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_10
# --- End of included input --- d_11The DISTANCES action with label d_11 calculates the following quantities:| Quantity | Type | Description |
| d_11 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_11_lowest | scalar | the smallest of the colvars |
: 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=383 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_11: DISTANCES GROUPA=383 GROUPB=memb LOWEST LOWMEM
d_11The DISTANCE action with label d_11 calculates the following quantities:| Quantity | Type | Description |
| d_11 | 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=383,572 ATOMS2the pair of atom that we are calculating the distance between=383,702 ATOMS3the pair of atom that we are calculating the distance between=383,832 ATOMS4the pair of atom that we are calculating the distance between=383,962 ATOMS5the pair of atom that we are calculating the distance between=383,1092
d_11_lowestThe LOWEST action with label d_11_lowest calculates the following quantities:| Quantity | Type | Description |
| d_11_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_11
# --- End of included input --- d_12The DISTANCES action with label d_12 calculates the following quantities:| Quantity | Type | Description |
| d_12 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_12_lowest | scalar | the smallest of the colvars |
: 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=417 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_12: DISTANCES GROUPA=417 GROUPB=memb LOWEST LOWMEM
d_12The DISTANCE action with label d_12 calculates the following quantities:| Quantity | Type | Description |
| d_12 | 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=417,572 ATOMS2the pair of atom that we are calculating the distance between=417,702 ATOMS3the pair of atom that we are calculating the distance between=417,832 ATOMS4the pair of atom that we are calculating the distance between=417,962 ATOMS5the pair of atom that we are calculating the distance between=417,1092
d_12_lowestThe LOWEST action with label d_12_lowest calculates the following quantities:| Quantity | Type | Description |
| d_12_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_12
# --- End of included input --- d_13The DISTANCES action with label d_13 calculates the following quantities:| Quantity | Type | Description |
| d_13 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_13_lowest | scalar | the smallest of the colvars |
: 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=448 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_13: DISTANCES GROUPA=448 GROUPB=memb LOWEST LOWMEM
d_13The DISTANCE action with label d_13 calculates the following quantities:| Quantity | Type | Description |
| d_13 | 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=448,572 ATOMS2the pair of atom that we are calculating the distance between=448,702 ATOMS3the pair of atom that we are calculating the distance between=448,832 ATOMS4the pair of atom that we are calculating the distance between=448,962 ATOMS5the pair of atom that we are calculating the distance between=448,1092
d_13_lowestThe LOWEST action with label d_13_lowest calculates the following quantities:| Quantity | Type | Description |
| d_13_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_13
# --- End of included input --- d_14The DISTANCES action with label d_14 calculates the following quantities:| Quantity | Type | Description |
| d_14 | vector | the DISTANCES between the each pair of atoms that were specified |
| d_14_lowest | scalar | the smallest of the colvars |
: 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=482 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=memb LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
# d_14: DISTANCES GROUPA=482 GROUPB=memb LOWEST LOWMEM
d_14The DISTANCE action with label d_14 calculates the following quantities:| Quantity | Type | Description |
| d_14 | 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=482,572 ATOMS2the pair of atom that we are calculating the distance between=482,702 ATOMS3the pair of atom that we are calculating the distance between=482,832 ATOMS4the pair of atom that we are calculating the distance between=482,962 ATOMS5the pair of atom that we are calculating the distance between=482,1092
d_14_lowestThe LOWEST action with label d_14_lowest calculates the following quantities:| Quantity | Type | Description |
| d_14_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=d_14
# --- End of included input --- sortedThe SORT action with label sorted calculates the following quantities:| Quantity | Type | Description |
| sorted.1 | scalar | the 1th largest of the input scalars |
| sorted.2 | scalar | the 2th largest of the input scalars |
| sorted.3 | scalar | the 3th largest of the input scalars |
| sorted.4 | scalar | the 4th largest of the input scalars |
| sorted.5 | scalar | the 5th largest of the input scalars |
| sorted.6 | scalar | the 6th largest of the input scalars |
| sorted.7 | scalar | the 7th largest of the input scalars |
| sorted.8 | scalar | the 8th largest of the input scalars |
| sorted.9 | scalar | the 9th largest of the input scalars |
| sorted.10 | scalar | the 10th largest of the input scalars |
| sorted.11 | scalar | the 11th largest of the input scalars |
| sorted.12 | scalar | the 12th largest of the input scalars |
| sorted.13 | scalar | the 13th largest of the input scalars |
| sorted.14 | scalar | the 14th largest of the input scalars |
| sorted.15 | scalar | the 15th largest of the input scalars |
: SORTThis function can be used to sort colvars according to their magnitudes. More details ARGthe values input to this function=d_0.lowest,d_1.lowest,d_2.lowest,d_3.lowest,d_4.lowest,d_5.lowest,d_6.lowest,d_7.lowest,d_8.lowest,d_9.lowest,d_10.lowest,d_11.lowest,d_12.lowest,d_13.lowest,d_14.lowest
metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=sorted.1,sorted.15 SIGMAthe widths of the Gaussian hills=0.05,0.05 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=5 PACEthe frequency for hill addition=200 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=323
GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=6.152625,6.152625
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metad: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=sorted.1,sorted.15 SIGMAthe widths of the Gaussian hills=0.05,0.05 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=5 PACEthe frequency for hill addition=200 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=323
GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=6.152625,6.152625
FILE a file in which the list of added hills is stored=HILLS
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rgThe GYRATION action with label rg calculates the following quantities:| Quantity | Type | Description |
| rg | 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=33,64,98,129,163,194,225,256,287,318,352,383,417,448,482
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:| Quantity | Type | Description |
| lwall.bias | scalar | the instantaneous value of the bias potential |
| lwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg ATthe positions of the wall=1.8 KAPPAthe force constant for the wall=10000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=sorted.1,sorted.15,rg,lwall.bias,metad.bias FILEthe name of the file on which to output these quantities=METADYN STRIDE the frequency with which the quantities of interest should be output=10000
