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 ?
Atsutoshi
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Ilyas Yildirim
Sent: Saturday, June 10, 2006 11:54 PM
To: amber.scripps.edu
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) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Wed Jun 21 2006 - 06:07:04 PDT
