Joe,
It has always been that the fractional and cartesian-wrapped coordinates
were only used inside pme.
The wrapped coords are saved between steps I think, so they could be
available outside, but the fractional coords are generated at each step.
Even so, they would only be good between calling pme and the integration
step, after which they would be for the last step.
The X coordinates are the unwrapped coordinates.
Mike
On 4/6/09 8:48 AM, "Joe Krahn" <krahn.niehs.nih.gov> wrote:
> How are the coordinates managed in Sander? Bob Duke said there are three
> forms, which I assume are:
> 1) actual orthogonal coordinates
> 2) orthogonal wrapped coordinates (wrapped into periodic box)
> 3) fractional wrapped coordinates
>
> Are these all available during force calculations, or are some only
> generated locally -- i.e. is fractional only within Ewald code?
>
> What coordinates are represented by X in force.f? (Where the global X is
> named XX to aid in the confusion.)
>
> For X-ray forces, I can generally follow Ewald, which is very similar to
> X-ray force calculation, but it would be good to have some of the
> overall Sander design issues documented, even if it is in a
> quick-and-dirty form.
>
> This is the sort of thing that I think is appropriate to describe on the
> Wiki. The purpose of a Wiki is to avoid the need for a formal maintainer
> (most of the time) and anyone who thinks they know how something works
> can write in some information, and other people can update that
> information to develop a complete picture. It can also evolve over time,
> where anyone working on code in a given area can add more info, or put
> comments about things that need work.
>
> There is probably a lot of answers in the amber-dev mailing list
> archive. A simple way to collect some of the more useful posts, without
> spending extra time to organize them or worry about pretty formatting,
> is to start a simple FAQ section in the Wiki. Does that sound good to
> other developers?
>
> Also, I started a File Format section on the Wiki, with a side-bar link.
> It is incomplete (i.e. what is TEMP0 in the restart file?) When it is
> more complete, maybe it can get added to the manual.
>
> Joe
>
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Received on Wed Apr 08 2009 - 01:12:09 PDT
