Hi,
Why do you need an average structure of a water box? This seems strange to
me since all of the rotation and translation undergone by the water over
the course of a simulation will result in something strange. The average
command is of more use (in my opinion) when looking at solute molecules,
and even then you do something like RMS-fit prior to averaging to remove
global rotational/translational motion.
On Mon, Jul 13, 2015 at 9:38 AM, Robert Molt <rwmolt07.gmail.com> wrote:
>
> center :1-550
> image familiar
>
It is recommended that autoimage be used instead of center/image in most
cases.
-Dan
> average Water_550_Average.pdb pdb
>
> The structure I get is a very sparse water box. I obviously am not
> imaging properly the water molecules from the "center" box (for lack of
> knowing what to call it). My understanding is that "image" puts all
> waters in the "center" box, "familiar" is necessary for a truncated
> octahedron. Is my mistake obvious to anyone?
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
> Nigel Richards Research Group
> Department of Chemistry & Chemical Biology
> Indiana University-Purdue University Indianapolis
> LD 326
> 402 N. Blackford St.
> Indianapolis, IN 46202
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jul 13 2015 - 09:30:04 PDT
