Subject: RE: trajectory file conversion (update)

From: "Leif Laaksonen" <[email-masked]>
Date: Fri, 22 Mar 2002 10:19:47 +0200

I'm sorry but I made a mistake because I was in the believe that 
we talked about the representation in which the trajectories are
saved on the the disk. The internal representation inside CHARMM/CHARMm
is REAL*8 but the trajectories are saved on the disk in REAL*4.
Am I right?

-leif laaksonen

-----Original Message-----
From: Computational Chemistry List [mailto:[email-masked]] On
Behalf Of Rick Venable
Sent: Friday, March 22, 2002 4:50 AM
To: CCL
Cc: Dr. Richard L. Wood; Jim Phillips
Subject: CCL:trajectory file conversion (update)

The f.p. difference I mentioned for CHARMM vs. CHARMm would seem to be
historical; both use double precision (REAL*8) for coordinate and other
f.p. numbers, and have for some time (years).  I have not yet determined
why I had problems with flipdcd previously-- but I plan to try again
> from source (rather than pre-compiled Linux binary).

I should also note that the trajectory transfer format (produced by DYNA
FORMAT, converted back to binary via DYNA UNFORMAT) was changed at ca.
CHARMM v. 27, in a way that lost backwards compatibility.  It is
strongly recommended that the same CHARMM version be used on both
machine types in order to accomplish trajectory transfer via this
mechanism.

Finally, I should note that while CHARMM is not free, it is available as
academically licensed source for a modest fee, a well crafted letter,
and a bit of patience.  Here's the information from the Karplus group:

	-----------------------------------------------------

We distribute the source code of the CHARMM program with documentation
to individual academic research groups for a $600 licensing fee. CHARMM
runs on a variety of UNIX workstations, including the SG Indigo
machines. No graphics are necessary. The present version of the program
being distributed is C28.

The license is issued to the head of a laboratory or research group.
Please send a letter with the full name and title of the professor in
charge of your group and formal mailing address. Describe briefly the
kind of research for which you intend to use the CHARMM program and the
computers you will be using. The letter should be addressed to:

The CHARMM Development Project
Professor Martin Karplus
Department of Chemistry & Chemical Biology
12 Oxford Street
Harvard University
Cambridge, Massachusetts 02138

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From: Rick Venable <[email-masked]>
Date: Fri, 22 Mar 2002 11:18:35 -0500

> is REAL*8 but the trajectories are saved on the disk in REAL*4.

Yes and no, it turns out.  While coordinates are converted to REAL*4 for
storage, unit cell data is stored as REAL*8 when the simulation used the
CRYSTAL facility for periodic boundary conditions.

For these trajectories, the 11th element of the 20 element INTEGER*4
header is set to 1, and the X, Y, and Z coordinate arrays are preceded
by a 6 element REAL*8 array for each stored trajectory frame.  I suspect
that may be the root cause of the problems I had with flipdcd.

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