[gmx-users] dummy atoms for amber free energy

[Maik Goette]

Hi David

That's also a point of discussion in our group.
My personal opinion is, that a mass, which is connected via e.g. the 
bond potential would fluctuate in the harmonic function and those energy 
terms should cancel out over time. For the dummy-masses have no other 
interactions, there won't occur any frictional energy contribution.
So everything should be fine.
Anyway, grompp don't like 0 masses. This may be, because F/m=a and this 
would lead to a division with 0, which isn't defined. I never tried to 
compare a run with full dummy masses and masses set to small values, 
e.g. 0.001.

For this is very intuitive, I would be very thankful for every hint to 
literature regarding this aspect.:)

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/


David Mobley wrote:
> 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 state.
> 
> Thanks,
> David
> 
> 
> On 2/6/06, *Maik Goette* <mgoette at mpi-bpc.mpg.de 
> <mailto:mgoette at mpi-bpc.mpg.de>> wrote:
> 
>     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 <http://bpc.mpg.de>
>              mgoette2[at]gwdg.de
>     WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
> 
> 
>     mernst at tricity.wsu.edu <mailto: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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