AMBER Archive (2004)

Subject: Re: AMBER: Molecular Frame

From: David A. Case (
Date: Fri Jan 02 2004 - 10:22:10 CST

On Thu, Jan 01, 2004, Byungchan Kim wrote:
> Can anyone explain of the molecular frame and how can I calculate it
> from the trajectory of molecular dynamics?
> I tried to find from web but there is no clear definition or explanation.

It's not clear what information you are looking for, or where the term
"molecular frame" comes from. You can use ptraj or carnal to superimpose
snapshots of an md simulation onto a common "frame", pretty much removing
overall translation and rotation. Analysis of such superimposed snapshots
would then be said to be in a "molecular frame".

..hope this helps...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to