[gmx-users] dummy atoms for amber free energy

[mernst at tricity.wsu.edu]

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