On Mon, Apr 06, 2009, Joe Krahn 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?
I don't think 2 or 3 (above) are generally available, outside specific
routines(?)
>
> What coordinates are represented by X in force.f? (Where the global X is
> named XX to aid in the confusion.)
These are 1): actual orthogonal coordinates.
>
> 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?
Yes...indeed does sound good.
>
> 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.
It's for replica exchange...Dan or Carlos (etc) can explain better,
and/or just update the wiki.
...thanks for getting this all going....dave
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Received on Wed Apr 08 2009 - 01:11:35 PDT
