Re: ANAL Questions!

From: <ross_at_cgl.ucsf.EDU>
Date: Wed 14 Jul 1999 19:20:49 -0700 (PDT)

        1. ANAL does not have PME feature incorporated into it, so how is
        long-range electrostatic interactions handled? Will it be ignored if the
        distance between 2 charges greater than the cutoff distanceb (using the


        If so, How big is the cutoff distance sufficient in order to
        achieve acceptable accuracy (e.g. Rcut = 15.0 (A)?)

The cutoff should maybe be less than the shortest box dimension,
and perhaps for solute systems that remain integral within the
box, the box should be ignored and iftres=0 (all solute-solute
interactions used).

What does "acceptable accuracy" mean? If you are trying to analyze
PME potentials with a pairwise-only method, you have to consider
that you are comparing a local pairwise interaction (non-PME) to
an infinite lattice of pairwise interaction. The good news is that,
unless you are really interested in a crystalline situation, the
pairwise analysis may be more like reality. The effect of say 8A
vs 10A cutoff can be determined in this situation by doing both
calcs and comparing energies. In general, I believe that the
consensus is that the contribution beyond 9-10A is small
energetically but important for getting a trajectory right on a
very long time scale.

        2. ANAL contains bug, as shown on AMBER webpage, that is not consistant
        with SANDER in computing energy. Can anyone tell how serious it is? I'd
        like to use ANAL to compare energies of different sub-systems. Can
        anyone give me your opinions on this?

I'm looking forward to opinions here myself. :-)

Bill Ross
Received on Wed Jul 14 1999 - 19:20:49 PDT
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