Project ID: plumID:21.000
Source: plumed.dat
Originally used with PLUMED version: 2.4
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
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WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-8843 # include toxin for appropriate RMSD/COM calcs
############################################## ############## DEFINE RESIDUES ############### ##############################################
### toxin (heavy) toxin: 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=8824,8825,8826,8827,8828,8829,8830,8831,8838,8839,8840,8841,8842,8843 toxin_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=toxin LEU383: 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=6012,6014,6016,6019,6021,6025,6029,6030 LEU383_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=LEU383 ILE384: 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=6031,6033,6035,6037,6041,6044,6048,6049 ILE384_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=ILE384 ASN387: 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=6089,6091,6093,6096,6097,6098,6101,6102 ASN387_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=ASN387 PHE399: 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=6283,6285,6287,6290,6291,6293,6295,6297,6299,6301,6302 PHE399_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=PHE399 LEU403: 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=6344,6346,6348,6351,6353,6357,6361,6362 LEU403_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=LEU403 ARG406: 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=6398,6400,6402,6405,6408,6411,6413,6414,6417,6420,6421 ARG406_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=ARG406 TYR407: 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=6422,6424,6426,6429,6430,6432,6434,6435,6437,6439,6441,6442 TYR407_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=TYR407 LYS410: 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=6479,6481,6483,6486,6489,6492,6495,6499,6500 LYS410_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=LYS410 LEU426: 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=6732,6734,6736,6739,6741,6745,6749,6750 LEU426_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=LEU426 VAL429: 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=6780,6782,6784,6786,6790,6794,6795 VAL429_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=VAL429 LEU449: 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=7079,7081,7083,7086,7088,7092,7096,7097 LEU449_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=LEU449 SER485: 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=7653,7655,7657,7660,7662,7663 SER485_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=SER485 ### calph COM for relevant helices helix1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5707,5722,5732,5753,5763,5785,5801,5821,5833,5848,5868,5898,5904,5923,5939,5954,5977,5983,6000,6014,6033,6052,6074,6091,6105,6115,6130,6149,6169,6184 helix2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6242,6263,6285,6305,6322,6336,6346,6365,6384,6400,6424,6445,6459,6481,6503 helix3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7533,7549,7563,7587,7619,7625,7635,7655,7666,7676 ############################################### ############### DEFINE COLVARS ################ ###############################################
### protein-ligand dists LEU383_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=LEU383_com,toxin_com ILE384_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ILE384_com,toxin_com ASN387_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ASN387_com,toxin_com PHE399_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=PHE399_com,toxin_com LEU403_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=LEU403_com,toxin_com ARG406_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ARG406_com,toxin_com TYR407_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=TYR407_com,toxin_com LYS410_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=LYS410_com,toxin_com LEU426_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=LEU426_com,toxin_com VAL429_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=VAL429_com,toxin_com LEU449_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=LEU449_com,toxin_com SER485_com_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SER485_com,toxin_com ### protein-protein backbone distances h1_h2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix1,helix2 h1_h3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix1,helix3 h2_h3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix2,helix3 # make STRIDE = to your exchange attempt frequency!!! PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1