Re: [AMBER] Excluded atoms list

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 24 Nov 2010 14:56:12 -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?

You could read the code, put in trace statements maybe. If you're
hacking prmtops, you almost owe it to yourself :-)

What you are attempting sounds logical. For an experiment you could
remove the excluded lists and see if that has an effect.


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Received on Wed Nov 24 2010 - 15:00:04 PST
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