Project ID: plumID:22.000
Source: plumed-common-3.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
UNITSThis command sets the internal units for the code. More detailsLENGTH=nmthe units of lengthsTIME=psthe units of timeENERGY=kj/molthe units of energyMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=3.pdba file in pdb format containing a reference structureRANDOM_EXCHANGESSet random pattern for exchanges. More details
hbond:CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=427,363the atoms involved in each of the contacts you wish to calculateSWITCH1={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT1=0.09091A weight value for a given contact, by default is 1ATOMS2=405,346the atoms involved in each of the contacts you wish to calculateSWITCH2={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT2=0.09091A weight value for a given contact, by default is 1ATOMS3=383,330the atoms involved in each of the contacts you wish to calculateSWITCH3={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT3=0.09091A weight value for a given contact, by default is 1ATOMS4=364,311the atoms involved in each of the contacts you wish to calculateSWITCH4={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT4=0.09091A weight value for a given contact, by default is 1ATOMS5=347,297the atoms involved in each of the contacts you wish to calculateSWITCH5={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT5=0.09091A weight value for a given contact, by default is 1ATOMS6=331,278the atoms involved in each of the contacts you wish to calculateSWITCH6={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT6=0.09091A weight value for a given contact, by default is 1ATOMS7=312,262the atoms involved in each of the contacts you wish to calculateSWITCH7={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT7=0.09091A weight value for a given contact, by default is 1ATOMS8=298,243the atoms involved in each of the contacts you wish to calculateSWITCH8={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT8=0.09091A weight value for a given contact, by default is 1ATOMS9=279,227the atoms involved in each of the contacts you wish to calculateSWITCH9={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT9=0.09091A weight value for a given contact, by default is 1ATOMS10=263,213the atoms involved in each of the contacts you wish to calculateSWITCH10={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT10=0.09091A weight value for a given contact, by default is 1ATOMS11=244,203the atoms involved in each of the contacts you wish to calculateSWITCH11={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT11=0.09091A weight value for a given contact, by default is 1SUMcalculate the sum of all the contacts in the input
alpha:ALPHARMSDProbe the alpha helical content of a protein structure. More detailsRESIDUES=28-39this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedR_0=0.1The r_0 parameter of the switching functionD_0=0.02 app_head:The d_0 parameter of the switching functionCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=230,246 app_tail:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=407,429 distance:the group of atoms that you are calculating the Gyration Tensor forDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=app_head,app_tailthe pair of atom that we are calculating the distance between