[gmx-users] dummy atoms for amber free energy
dmobley at gmail.com
Mon Feb 6 18:09:50 CET 2006
Just out of curiousity, since you seem to know something about this, Maik...
If you don't turn off the mass, doesn't it mean that there are energetic
contributions from (for example) bond vibrations and things which are still
left in in the end state? I usually do absolute binding free energy
calculations so I'm not too up on how people correct for the fact that they
have non-interacting dummy atoms which are still bonded to things in the end
On 2/6/06, Maik Goette <mgoette at mpi-bpc.mpg.de> wrote:
> 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
> > 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
> > 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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