Beijing Ryan Researchsoftware and Technology Center

To define a reaction coordinate for further usage, like in command “steer”, “fourierpath” and "lambdady".

Examples

#to define a distance type reaction coordinate

reactcoord type=dist \

name="posDMSO" \

verbose=true \

group1="segid proa && seq 26 82 99 59 56 55 46 \

&& ! type N C O HN CA HA* " \

group2="resname DMS"

Keywords

type=<rc type>	Available types are: Dist displacement between two groups Zcom Z directions displacement only Ycom Y directions displacement only Xcom X directions displacement only Angle angle among three groups Dihe dihedral angle defined by four groups RMSD RMSD to ref1 dRMSD the difference between RMSD to ref1 and RMSD to ref2 RGY radius of gyration of atoms group selected
Name=<name>	To assign a unique name for later quoting
Select=<select expr>	Type “Dist” and “Zdist” need 2 selections Type “Angle” need 3 selections Type “Dihe” need 4 selections Type “RMSD” and “dRMSD” need two selections, the first one for superimpose and the other one for RMSD calculation Type “RGY” need 1 selection only.
Verbose=<bool>	Whether printing the details about the RC defined

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