Deear mister Ben,
I don't know if your mail is serious, however I find your system very
interesting. Personally we think you mail might be joke, however I will do
besst I can do helping you. My professor had once similar good idea. We are
currently implementing relativistic equations of motion (lorentz
transformations) for gromacs 5.0.
One could actually very interestingly study absortion of protein on black
whole surface and calculate free energies.
On other next interesting thing, my professor also expect that photo
driven processes in protein as studied here:
G. Groenhof, L.V. Schaefer, M. Boggio-Pasqua, H. Grubmueller and M.A. Robb.
Arginine52 controls the photoisomerization process in photoactive yellow
protein.
Journal of Americal Chemical Society, 130 (2008), 3250-3251.
Will be affected by presence of blackhole. Soon or later such kind event
might become realistic and China should be the first to work on it.
However there is now experimental data to paramatrize such systems,
especialy not under newtonian law. A difficult with black holes is to
intepretate experiments results, as there are no distinction between blackhole
of mater or anti-matter.
First one thing:
For proper solvent, currently me and my professor applied for grant for
start working on the 'silent ether' forcefield, if interested you can contact
us off list. Although many people claim silent ether is not a realistic model,
we will only use it as an emperical solvator to avoid complicated fysical
effects.
Second one next thing:
For box to minimize the ammount of silent ether I think the best choice can
be found here:
Henk Bekker, Jur P. van den Berg, TSJERK A. WASSENAAR: Constructing a
Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with
Periodic Boundary Conditions. International Conference on Computational Science
2003: 70-79
Thrid one more next thing:
For force field of black holes you should consider chose poper density,
mass and Schwarz-schild radius.
But make sure mass stays in withinTolman-Oppenheimer-Volkoff limit.
Fourth one final last thing:
>Could two black wholes see each other if box too small?
Shuch problem only occurs when using PME (threating "no hair" theorem).
For pressure virial law should still hold, with minor relativistic
corrections.
Other important next thing after last thing:
Don't remove angular momentum each step, as they form together with its
mass an important classification for black hole. The silent ether added will
prevent flying ice cube problems.
For temperature be carefull to use older gromacs version (3.3), as the
underestimate the proper temperature ensemble in system !!!!!!
Good luck,
greetings
Jiang,
roger han wrote:
> Dear mister gromacs
>
> My professor interested in black wholes. How can I put a particle in a box
and set mass to infinity? Which solvent is best choice and could there be
problems with pressure? I'm also not sure about periodic boundaries. Could two
black wholes see each other if box too small?
>
> Many thanks
>
> Ben
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