VMD-L Mailing List

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 23 2004 - 12:39:42 CDT

On Tue, Jun 22, 2004, Kamp, Marc vander wrote:
>
> You are right, I turns out to be a rst7 file after all.
> I just assumed it was a crd-file, because I got it by using the
> saveamberparm command in tleap (or actually teLeap), the program used in
> AMBER to build the parmtop-files.

The Amber community does not have a universal nomenclature for what such
files are called. Here is a glossary:

A "restart" file has only one configuration (set of coordinates). It may or
may not have velocity and box information as well. In spite of its name,
it can be created by LEaP as an initial file for simulations. Amber users
often name the file that LEaP creates "prmcrd" (by analogy to "prmtop"), but
that is not required. Of course, it is often loosely referred to as a
"coordinate file".

A "trajectory" file has (potentially) lots of snapshots (configuations), and
is something that can be animated. The default name for this file is "mdcrd"
(for molecular dyanmics coordiantes), but most(?) Amber users name this as
foo.trj, or something similar. Nevertheless, many Amber users give this sort
of file a foo.crd name, and/or call it a "crd file".

The important distinction is whether the file can contain just one
configuration, or can contain many.

Of course, people have been talking for years about getting a common format
for such information. Those people who have been holding their breath waiting
for this to happen have long since expired.....

For obvious reasons, we are reluctant to change file formats, since that
breaks lots of programs that use these files. The formats were static for
many years, but in 2002 (for Amber7) we realized that we could no longer
live with the (ancient) formats that were limited to fewer than 100,000 atoms.
This led to a major change in the prmtop format, a very minor (but annoying
to many!) change in the restart format, and no change to the trajectory
format.

...hope this helps...dac 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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