AMBER Archive (2006)

Subject: RE: AMBER: Simulating a periodic crystal

From: Jiang Jianwen (chejj_at_nus.edu.sg)
Date: Fri Mar 31 2006 - 05:31:47 CST

> In the papers of Darden, a unit cell was replicated to mimic the
crystal.
> Either one or four (or eight?) copies of the crystal periodic unit
cell were
> explicitly present representing the crystal structure. This works
because
> there are no bonds between elements of the primary unit cell and its
> periodic images (i.e. the system was not infinite).

Dear Prof. Cheatham,

Do you mean the crystal structure with either one or four (or eight)
copies of the periodic unit cell is entirely immersed in large
simulation box of solvent? By this, I can understand that all the
biomolecules are inside one box, and no covalent bonds cross the
boundary.

> Mimimally to get the infinite helix to work, code would need to be
modified
> to include the extra bonds between the periodic unit cells; this
would
> require either adding periodic imaging to the bond, angle and dihedral

> routines or (as done in CHARMM) creation of virtual copies of the
images.
> Extending the code in this manner will not be trivial and will involve
changes
> to the prmtop (LEaP), sander (and accessory programs like anal,
nmode, ...).

> In the earlier post, DAC mentioned that he believed that CHARMM can do
> this; it can, at least within the CRYSTAL/IMAGE facility and it can
also
> impose symmetry, for example treating only 1/60th of a 60-fold
symmetric
> virus particle and imposing symmetry on the rest (see work by C. Post

> and/or BR Brooks).

It seems that CHARMM, Gromos, Gromas or NAMD can do simulation for
infinitely large periodic protein crystals, right?

Thank you so much for your generous helps.

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