Project ID: plumID:22.013
Source: plumed/6e1w/production/plumed.production.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
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=reference.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=rna
The MOLINFO action with label calculates somethingres18The COM action with label res18 calculates the following quantities:| Quantity | Type | Description |
| res18 | 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=@sugar-18the heavy atoms of the sugar in residue 18. Click here for more information.
res2The COM action with label res2 calculates the following quantities:| Quantity | Type | Description |
| res2 | 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=@sugar-2the heavy atoms of the sugar in residue 2. Click here for more information.
res31The COM action with label res31 calculates the following quantities:| Quantity | Type | Description |
| res31 | 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=@sugar-31the heavy atoms of the sugar in residue 31. Click here for more information.
res23The COM action with label res23 calculates the following quantities:| Quantity | Type | Description |
| res23 | 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=@sugar-23the heavy atoms of the sugar in residue 23. Click here for more information.
res5The COM action with label res5 calculates the following quantities:| Quantity | Type | Description |
| res5 | 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=@sugar-5the heavy atoms of the sugar in residue 5. Click here for more information.
res6The COM action with label res6 calculates the following quantities:| Quantity | Type | Description |
| res6 | 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=@sugar-6the heavy atoms of the sugar in residue 6. Click here for more information.
res29The COM action with label res29 calculates the following quantities:| Quantity | Type | Description |
| res29 | 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=@sugar-29the heavy atoms of the sugar in residue 29. Click here for more information.
res18_l_C7_1070The DISTANCE action with label res18_l_C7_1070 calculates the following quantities:| Quantity | Type | Description |
| res18_l_C7_1070 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=res18,1070
res2_l_C5_1067The DISTANCE action with label res2_l_C5_1067 calculates the following quantities:| Quantity | Type | Description |
| res2_l_C5_1067 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=res2,1067
res31_l_C8_1073The DISTANCE action with label res31_l_C8_1073 calculates the following quantities:| Quantity | Type | Description |
| res31_l_C8_1073 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=res31,1073
res23_l_C5_1067The DISTANCE action with label res23_l_C5_1067 calculates the following quantities:| Quantity | Type | Description |
| res23_l_C5_1067 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=res23,1067
res5_l_C4_1066The DISTANCE action with label res5_l_C4_1066 calculates the following quantities:| Quantity | Type | Description |
| res5_l_C4_1066 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=res5,1066
res6_l_C4_1066The DISTANCE action with label res6_l_C4_1066 calculates the following quantities:| Quantity | Type | Description |
| res6_l_C4_1066 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=res6,1066
res29_l_C7_1070The DISTANCE action with label res29_l_C7_1070 calculates the following quantities:| Quantity | Type | Description |
| res29_l_C7_1070 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=res29,1070
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=rc1The COMBINE action with label rc1 calculates the following quantities:| Quantity | Type | Description |
| rc1 | scalar | a linear compbination |
ARGthe values input to this function=res18_l_C7_1070,res2_l_C5_1067,res31_l_C8_1073,res23_l_C5_1067,res5_l_C4_1066,res6_l_C4_1066,res29_l_C7_1070 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1,1,1 COEFFICIENTS the coefficients of the arguments in your function=-0.22535330057144165,-0.4727707505226135,0.4952104985713959,-0.2616001069545746,-0.26277562975883484,-0.006056515965610743,0.5856176018714905 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cnThe COORDINATIONNUMBER action with label cn calculates the following quantities:| Quantity | Type | Description |
| cn | vector | the coordination numbers of the specified atoms |
| cn_max | scalar | the maximum colvar |
| cn_mean | scalar | the mean of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1063-1085 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-1062 NN The n parameter of the switching function =4 R_0The r_0 parameter of the switching function=0.3 MAXcalculate the maximum value={BETA=0.1} MEAN calculate the mean of all the quantities
cn: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1063-1085 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-1062 NN The n parameter of the switching function =4 R_0The r_0 parameter of the switching function=0.3 MAXcalculate the maximum value={BETA=0.1} MEAN calculate the mean of all the quantities D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
# cn: COORDINATIONNUMBER SPECIESA=1063-1085 SPECIESB=1-1062 NN=4 R_0=0.3 MAX={BETA=0.1} MEAN
cn_grpThe GROUP action with label cn_grp calculates the following quantities:| Quantity | Type | Description |
| cn_grp | 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=1063-1085
cn_matThe CONTACT_MATRIX action with label cn_mat calculates the following quantities:| Quantity | Type | Description |
| cn_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1063-1085 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=1-1062 R_0The r_0 parameter of the switching function=0.3 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =4 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_onesThe CONSTANT action with label cn_ones calculates the following quantities:| Quantity | Type | Description |
| cn_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=1062
cnThe MATRIX_VECTOR_PRODUCT action with label cn calculates the following quantities:| Quantity | Type | Description |
| cn | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cn_mat,cn_ones
cn_caverageThe MEAN action with label cn_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_caverage | 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=cn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_me_maxThe CUSTOM action with label cn_me_max calculates the following quantities:| Quantity | Type | Description |
| cn_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=cn FUNCthe function you wish to evaluate=exp(x/0.1) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_mec_maxThe SUM action with label cn_mec_max calculates the following quantities:| Quantity | Type | Description |
| cn_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=cn_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_maxThe CUSTOM action with label cn_max calculates the following quantities:| Quantity | Type | Description |
| cn_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cn_mec_max FUNCthe function you wish to evaluate=0.1*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_meanThe MEAN action with label cn_mean calculates the following quantities:| Quantity | Type | Description |
| cn_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=cn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
rmsd1The RMSD action with label rmsd1 calculates the following quantities:| Quantity | Type | Description |
| rmsd1 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd1: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd2The RMSD action with label rmsd2 calculates the following quantities:| Quantity | Type | Description |
| rmsd2 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd2: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd3The RMSD action with label rmsd3 calculates the following quantities:| Quantity | Type | Description |
| rmsd3 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd3: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd4The RMSD action with label rmsd4 calculates the following quantities:| Quantity | Type | Description |
| rmsd4 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd4.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd4: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd4.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd5The RMSD action with label rmsd5 calculates the following quantities:| Quantity | Type | Description |
| rmsd5 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd5.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd5: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd5.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd6The RMSD action with label rmsd6 calculates the following quantities:| Quantity | Type | Description |
| rmsd6 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd6.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd6: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd6.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd7The RMSD action with label rmsd7 calculates the following quantities:| Quantity | Type | Description |
| rmsd7 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd7.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd7: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd7.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd8The RMSD action with label rmsd8 calculates the following quantities:| Quantity | Type | Description |
| rmsd8 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd8.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd8: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd8.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd9The RMSD action with label rmsd9 calculates the following quantities:| Quantity | Type | Description |
| rmsd9 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd9.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd9: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd9.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd10The RMSD action with label rmsd10 calculates the following quantities:| Quantity | Type | Description |
| rmsd10 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd10.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd10: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd10.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd11The RMSD action with label rmsd11 calculates the following quantities:| Quantity | Type | Description |
| rmsd11 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd11.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd11: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd11.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd12The RMSD action with label rmsd12 calculates the following quantities:| Quantity | Type | Description |
| rmsd12 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd12.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd12: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd12.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd13The RMSD action with label rmsd13 calculates the following quantities:| Quantity | Type | Description |
| rmsd13 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd13.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd13: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd13.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd14The RMSD action with label rmsd14 calculates the following quantities:| Quantity | Type | Description |
| rmsd14 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd14.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd14: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd14.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd15The RMSD action with label rmsd15 calculates the following quantities:| Quantity | Type | Description |
| rmsd15 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd15.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd15: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd15.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd16The RMSD action with label rmsd16 calculates the following quantities:| Quantity | Type | Description |
| rmsd16 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd16.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd16: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd16.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd17The RMSD action with label rmsd17 calculates the following quantities:| Quantity | Type | Description |
| rmsd17 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd17.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd17: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd17.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd18The RMSD action with label rmsd18 calculates the following quantities:| Quantity | Type | Description |
| rmsd18 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd18.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd18: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd18.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd19The RMSD action with label rmsd19 calculates the following quantities:| Quantity | Type | Description |
| rmsd19 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd19.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd19: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd19.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd20The RMSD action with label rmsd20 calculates the following quantities:| Quantity | Type | Description |
| rmsd20 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd20.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd20: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd20.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd21The RMSD action with label rmsd21 calculates the following quantities:| Quantity | Type | Description |
| rmsd21 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd21.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd21: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd21.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd22The RMSD action with label rmsd22 calculates the following quantities:| Quantity | Type | Description |
| rmsd22 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd22.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd22: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd22.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd23The RMSD action with label rmsd23 calculates the following quantities:| Quantity | Type | Description |
| rmsd23 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd23.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd23: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd23.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd24The RMSD action with label rmsd24 calculates the following quantities:| Quantity | Type | Description |
| rmsd24 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd24.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd24: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd24.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd25The RMSD action with label rmsd25 calculates the following quantities:| Quantity | Type | Description |
| rmsd25 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd25.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd25: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd25.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd26The RMSD action with label rmsd26 calculates the following quantities:| Quantity | Type | Description |
| rmsd26 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd26.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd26: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd26.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd27The RMSD action with label rmsd27 calculates the following quantities:| Quantity | Type | Description |
| rmsd27 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd27.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd27: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd27.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd28The RMSD action with label rmsd28 calculates the following quantities:| Quantity | Type | Description |
| rmsd28 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd28.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd28: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd28.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd29The RMSD action with label rmsd29 calculates the following quantities:| Quantity | Type | Description |
| rmsd29 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd29.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd29: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd29.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd30The RMSD action with label rmsd30 calculates the following quantities:| Quantity | Type | Description |
| rmsd30 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd30.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd30: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd30.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd31The RMSD action with label rmsd31 calculates the following quantities:| Quantity | Type | Description |
| rmsd31 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd31.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd31: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd31.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd32The RMSD action with label rmsd32 calculates the following quantities:| Quantity | Type | Description |
| rmsd32 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd32.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd32: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd32.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd33The RMSD action with label rmsd33 calculates the following quantities:| Quantity | Type | Description |
| rmsd33 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd33.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd33: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PDB/rmsd33.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
COMMITTORDoes a committor analysis. More details ...
ARGthe labels of the values which is being used to define the committor surface=cn.max
STRIDE the frequency with which the CVs are analyzed=500
BASIN_LL1List of lower limits for basin #=0.0
BASIN_UL1List of upper limits for basin #=1.0
... COMMITTOR
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
| metad.rbias | scalar | the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram. |
| metad.rct | scalar | the reweighting factor c(t). |
ARGthe labels of the scalars on which the bias will act=rc1 SIGMAthe widths of the Gaussian hills=0.09 HEIGHTthe heights of the Gaussian hills=1.0 BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 PACEthe frequency for hill addition=2000
GRID_MINthe lower bounds for the grid=-4.96 GRID_MAXthe upper bounds for the grid=3.43 GRID_BINthe number of bins for the grid=200
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metad
ARGthe labels of the scalars on which the bias will act=rc1 SIGMAthe widths of the Gaussian hills=0.09 HEIGHTthe heights of the Gaussian hills=1.0 BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 PACEthe frequency for hill addition=2000
GRID_MINthe lower bounds for the grid=-4.96 GRID_MAXthe upper bounds for the grid=3.43 GRID_BINthe number of bins for the grid=200
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
FILE a file in which the list of added hills is stored=HILLS
... METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmsd1,rmsd2,rmsd3,rmsd4,rmsd5,rmsd6,rmsd7,rmsd8,rmsd9,rmsd10,rmsd11,rmsd12,rmsd13,rmsd14,rmsd15,rmsd16,rmsd17,rmsd18,rmsd19,rmsd20,rmsd21,rmsd22,rmsd23,rmsd24,rmsd25,rmsd26,rmsd27,rmsd28,rmsd29,rmsd30,rmsd31,rmsd32,rmsd33 STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=6e1w_rmsd
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=res18_l_C7_1070,res2_l_C5_1067,res31_l_C8_1073,res23_l_C5_1067,res5_l_C4_1066,res6_l_C4_1066,res29_l_C7_1070,cn.max,cn.mean,rc1,metad.bias,metad.rbias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=6e1w_COLVAR
