[gmx-users] dummy atoms for amber free energy

David Mobley dmobley at gmail.com
Fri Feb 3 23:45:53 CET 2006

I usually do this by defining a new atom type in the [ atomtypes ] section
at the top of my topology file which has the parameters I want (i.e. zero
charge, zero vdw interactions).


On 2/3/06, mernst at tricity.wsu.edu <mernst at tricity.wsu.edu> wrote:
> Dear gmx-users,
> The Pande group amber port does not contain any specially designated dummy
> atom type
> like DUM. It does however contain atom types that seem very similar, like
> MW. I have
> used MW as a dummy in a simulation where a hydrogen disappears (turns into
> a dummy
> atom), assigning it zero charge as well. Is this a reasonable
> substitution? It is my
> understanding that dummy atoms should have zero mass, zero charge, and
> zero vdw
> interactions, and that their bonded interactions are unimportant (can
> duplicate
> parameters of the atoms they are replacing) since in any case they will
> have no
> energetic impact, being massless in their final state. Of course there are
> no long-range
> interactions either with dispersion and electrostatic effects set to zero.
> Finally, I would like to thank everyone who has responded to my questions
> over the last
> few days. Your help has been invaluable in getting me up to speed in this
> new simulation
> environment.
> Matt Ernst
> Washington State University
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