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 - 01:09:32 PDT
