AMBER Archive (2006)

Subject: RE: AMBER: Umbrella sampling

From: Atsutoshi Okabe (
Date: Sun Jun 18 2006 - 05:14:10 CDT

Dear Ilyas,

Thank you for your response.

Particularly, I want to fix center of mass of one benzene molecule and
center of mass another small molecule on z-axis. In addition, I want to
restraint benzene plane vertically against z-axis through simulation.
Can I do it with Amber ? If so, could you please tell me how to do ?


-----Original Message-----
From: [] On Behalf Of
Ilyas Yildirim
Sent: Saturday, June 10, 2006 11:54 PM
Subject: Re: AMBER: Umbrella sampling

> And I want to fix this two molecule on one axis (eg, fix their centers of
> mass on y=0, z=0)
> How can I fix this two molecule on one axis with Amber program?
> I expect to give me any suggestions.

Check out the program 3DNA, if your molecule is composed of nucleic acids.

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to