Re: [AMBER] how to fix COM of a group of atoms?

From: Ming Tang <>
Date: Fri, 15 Jul 2016 07:03:56 +0000

Thank you Jason,

I want to fix the COM of the first alpha carbon atoms in three different chains of my collagen only, without fixing all the three alpha carbon atoms. Is this feasible in AMBER?
As during stretching, three chains in my collagen unwinds, fixing all the alpha atoms will affect the unwinding process. Thus, I want to fix the COM of them only.

Thank you

-----Original Message-----
From: Jason Swails []
Sent: Tuesday, 12 July 2016 3:35 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] how to fix COM of a group of atoms?

On Sun, Jul 10, 2016 at 8:45 PM, Ming Tang <> wrote:

> Thank you Himanshu,
> will ntr=1 and restraintmask fix all the atoms in the specified group
> or the centre of mass of the group only?

‚ÄčAll atoms in the group.


Jason M. Swails
AMBER mailing list
AMBER mailing list
Received on Fri Jul 15 2016 - 00:30:02 PDT
Custom Search