Example: Interchain Interaction Energy

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Example: Interchain Interaction Energy

The following example shows how to restrict the energy calculation to the interaction energy between two chains with segment identifiers “a" and “b." Only the energies and forces between the selected atoms are computed.

CONStraints INTEraction 
    ( segid a ) ( segid b ) 
END

This example does not include the intrachain energy. To include the intrachain energy, one should specify the following:

CONStraints INTEraction 
    ( segid a or segid b ) ( segid a or segid b ) 
END

The following example modifies the weight of the inter- and intrachain interactions in the Hamiltonian, applying a weight of 0.5 to the bond energies and forces and a factor of 0.75 to the other energy terms :

CONStraints INTEraction 
   ( segid a or segid b ) ( segid a or segid b ) WEIGhts * 0.75 bonds 0.5 END 
END

This example includes the intrasegment bond energy and the overall intersegment energy but excludes the intrasegment angle and dihedral, improper, and nonbonded terms from the Hamiltonian :

CONStraints
    INTEraction ( segid a ) ( segid b ) WEIGhts * 1. END 
    INTEraction ( segid a ) ( segid a ) WEIGhts * 0. bonds 1. END 
    INTEraction ( segid b ) ( segid b ) WEIGhts * 0. bonds 1. END 
END

Three double selections are set up, each with a different weighting scheme. The Hamiltonian is the sum of the three partial Hamiltonians. The result is to turn off the intrasegment interactions other than the bonds.

Xplor-NIH 2025-03-21