AMBER Archive (2006)

Subject: Re: AMBER: ptraj grid output

From: Thomas E. Cheatham, III (
Date: Thu Jan 19 2006 - 12:47:05 CST

> center :1-461 mass origin
> image origin center familiar
> grid wat.grid 200 0.5 200 0.5 200 0.5 :WAT_at_O

What is the reference frame for the molecule? If the molecule is tumbling
in space, that fixed water will move with the molecule, but the grid does
not, it is fixed at the first frames location.

What you need to do is to pick a frame of reference to fit all the
coordinates of the solute to (i.e. residues 1-461), but even better a
smaller region. If the water in question is in the same place with
respect to the biomolecule (say for example a side chain residue :100),
then the water will move with the side chain. The grid does not move, so
the density can be smeared across multiple grid elements. If you want to
be sure to have that water in the same grid element each at each snapshot,
the solute needs to be fit, probably

rms first mass :99-101

...however when doing this, waters interacting away from :99-101 may
become smeared over multiple grid elements. Smearing also occurs due to
constant pressure (box size fluctuations) in addition to molecule motion.

Hopefully this makes some sense. Note also that the grid is currently
offset with respect to the coordinates by 1/2 the grid spacing.


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