[gmx-users] Black whole simluations

Jiang ran ran_jiong_lang2 at hotmail.com
Wed Mar 19 13:35:27 CET 2008

    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,
    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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