Dear Prof. Cheatham-
Thanks for your reply..I have been reading yours and Prof. Darden's articles
on the subject...May I ask one more related question. When in PBCs we say
"infinitely repeated", what does it mean, how calculations are done on
infinite scale? I am not able to capture this concept...or its that only a
few copies of primary cell are repeated in x y z directions, as we see in
xleap log file below>>
>solvatebox reboxed7b TIP3PBOX 8
Solute vdw bounding box: 52.590 65.545 78.264
Total bounding box for atom centers: 68.590 81.545 94.264
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 4 y= 5 z= 6
Thanks in advance for your comments!
Regards.
Vineet
>From: "Thomas E. Cheatham, III" <cheatham.chpc.utah.edu>
>Reply-To: amber.scripps.edu
>To: amber.scripps.edu
>Subject: Re: AMBER: Non-Bonded Cutoff vs PME
>Date: Tue, 19 Apr 2005 17:47:10 -0600 (Mountain Daylight Time)
>I would add to this that likely this comment was taken out of context...
>
>In the context of minimum image boundary conditions (as implemented in
>SPASMS) and specific implementations of cutoffs, it *is* essential that
>the cutoff be smaller that half the box size since there is/was no code to
>handle the interaction of an atom and its image. In AMBER, for example,
>you cannot have a "cutoff" (or direct space interaction) that is larger
>than 1/2 the box size when in PBC since we have no support for handing the
>direct interaction with images outside a periodic box centered on that
>given atom.
>
>In CHARMM, however, (and likely other crystal codes) you can run a cutoff
>over multiple box images (within the IMAGE facility) as this is supported
>by making virtual copies of the unit cell such that you have all the atoms
>within a cutoff.
>
>So, is it truth? Within minimum boundary conditions and direct space
>interactions it is... The issue you are getting at is how does Ewald/vdw
>relate in the context of cutoff and interaction with images. The cutoff
>is applied for both the vdw and electrostatics and represents all of the
>direct space interactions (those within the cutoff directly interacting
>with the specific atom). In SPASMS, no interactions outside the cutoff
>were considered and various means could be applied to smooth or shift the
>energy (or in the case of CHARMM the force) at the cutoff to minimize the
>abrupt truncation. To get longer range interactions, you can use a larger
>cutoff, however in AMBER/SPASMS you are limited to minimum image.
>
>Ewald calculations are a means to get the full periodic interaction (for
>more detail, see Allen & Tildesley or Leach or google "ewald
>electrostatics"). This method implicitly include the image interactions,
>however this is done in reciprocal space (and is not subject to the
>concept of minimum image) and its accuracy relates to the sum over
>k-vectors (or in SPME, the grid, interpolation order, ...). In principle,
>you can do SPME over the vdw as well ! to also include (all) the image
>interactions as at one point was implemented in AMBER. Ewald works
>basically by screening the short-range (direct) interactions and then
>correcting for what is absent in reciprocal space. The magnitude of the
>screening is controlled by the kappa or beta constant. In AMBER, we
>choose the Ewald coefficient (beta) such that the error in the
>electrostatics at the cutoff is less than DSUM_TOL.
>
>Is this the right way to do things? I believe so, however others have
>proposed in the past that we can get away with atom-based force-shifted
>cutoffs in the 12A range, simpler cutoffs [see for example the recent
>debatable Biochemistry article by Beck and co-workers 44, 609 (2005)],
>reaction fields, isotropic periodic boundary conditions, twin-range
>cutoffs, ... and the list goes on. A consequence of applying Ewald (or
>PME) or even large cutoffs that include image interactions is that you
>directly are including the interaction of yourself with all of (or some
>of) your periodic images. This could lead to artifacts. For nice
>discussion of potential periodicity artifacts, see the various papers by
>Hunenberger. For discussion of cutoffs, see Steinbach & Brooks (~1995 and
>earlier). For discussion of cutoff artifacts, see Smith & Pettitt 1991,
>Bader & Chandler 1992, Feller et al 1996, Schreiber & Steinhauser 1992,
>Cheatham et al 1995.
>
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Received on Wed Apr 20 2005 - 10:53:00 PDT
