For 1), it really depends on what you want to do
Do you want to remove the angular momentum from the entire system, or
a part (such as solute)?
Also, please tell us which AMBER version you have, as that part of the
code has changed with different versions.
For 2), you might mean that you want to do a rigid-body fit of each frame
to some reference structure. I do this with the "ptraj" module
of AMBER using the "rms" command. I believe it is well documented in the
ptraj section of the manual.
Carlos
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Department of Chemistry Fax: (631) 632-1555
SUNY at Stony Brook Web: http://comp.chem.stonybrook.edu/carlos
Stony Brook, NY 11794-3400 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================
----- Original Message -----
From: <dkon_at_email.arizona.edu>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, July 24, 2001 2:15 PM
Subject: trajectory analysis
I have two questions that I hope someone can enlighten me on:
1. Is it possible to perform an AMBER simulation while taking out the
rigid body motion? (Subtracting angular momentum perdiodically)
2. Is it possible to take out rigid body motion from an AMBER
trajectory?
Thanks,
Dmitry
Received on Tue Jul 24 2001 - 12:22:24 PDT
