[gmx-users] dummy atoms for amber free energy

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Feb 6 12:49:04 CET 2006

Hi Matt

I am not sure, if there may occur errors because of MW is used as 
But it's really no big deal to insert a DUM with 0 mass and charge.
You can also create as much dummies with the masses you want as you like.
If you like, I can send you my entries...but as I said, it's really no 
problem to make some.
Nevertheless, you shouldn't make the mass disappear. just turn of VdW 
and electorstatics.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

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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