Re: AMBER: regarding rigid molecules

From: David A. Case <>
Date: Thu, 16 Oct 2008 07:06:42 -0400

On Thu, Oct 16, 2008, aneesh cna wrote:

> I am using Amber 9.0 for simulating a system with 3-site
> Carbon dioxide. I want to keep Carbon dioxide as rigid molecules through
> out the simulation. How to do this in Amber? How to mention this in the
> input file ?

You can use SHAKE to keep the individual molecules rigid. However, please
check your results carefully: CO2 is a linear molecule that requires special
attention to keep rigid. I'm not sure whether or not the Amber code as it
stands is suited to this problem. Maybe someone on the list has tried this.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Fri Oct 17 2008 - 05:10:35 PDT
Custom Search