CHARMM Development Project Forums User Discussion & Questions Setup, I/O, and Basic questions About changing nbond exclusion list

I would like to exclude the nbond interactions between some atoms of two residues, namely, some atoms in residue A and some atoms in residue B. How can I do that? It's not possible to do it in the topology file, because this is inter-residue interaction. Thanks a lot!

I believe the BLOCK facility may be the most direct method; see block.doc

I'm using BLOCK to do lambda dynamics simulation. The lambda variables are changing during the simulation. It looks like things below:

QLDM
LANG TEMP @TEMP
! blk lamb vel mass ref_E
LDIN 1 1.00 0.0 5.0 0.0
LDIN 2 0.25 0.0 5.0 0.0
LDIN 3 0.25 0.0 5.0 0.0
LDIN 4 0.25 0.0 5.0 0.0
LDIN 5 0.25 0.0 5.0 0.0

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I wonder if I can specify COEF in such kind of simulation.

Since the atoms in the two residues could be very close to each other, or even in the same place. "Divided by 0 error" could occur in such simulation. Therefore, it is better to exclude the energy terms from calculation than to scale them.