[gmx-users] dummy atoms for amber free energy

[Maik Goette]

Hi Matt

I am not sure, if there may occur errors because of MW is used as 
water-dummy.
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.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.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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