[AMBER] Excluded atoms list

From: Jason S Grosch <jgrosch.ucsd.edu>
Date: Wed, 24 Nov 2010 14:41:57 -0800


I'm attempting to alter specific molecular interactions such that some atoms from different residues do not interact via charges or Lennard-Jones. I thought that altering the excluded atoms list in the topology file would be the way to accomplish this, but regardless of what I do to the excluded atoms list, keeping the number of excluded atoms list consistent, the energy is always the same. For example: running a simulation with two CO2 molecules with all atoms excluded has exactly the same energy as the unadjusted topology file. The only difference between the two md.out files is ~ 1kb of allocated memory. Does the excluded atoms list do anything? There is little information on this. Also, if this is not the way to remove specific charge and LJ interactions, is this possible to do?

Any assistance appreciated,
Jason Grosch

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Received on Wed Nov 24 2010 - 15:00:03 PST
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