RE: [AMBER] Umbrella Sampling

From: Seetin, Matthew <>
Date: Thu, 16 Jul 2009 21:13:59 +0100

Alternatively, you can ignore the iat variables and define the restraint as follows:

restraint="distance(com(:[residue].[atom name],...), com([atom numbers of molecule]) )

Omitting the brackets and supplying the residue numbers, atom names, and atom numbers as appropriate. There are further examples and clarification of this more human-readable scheme in section 6.1 of the manual should you find this a little easier.

--Matt Seetin

-----Original Message-----
From: on behalf of case
Sent: Thu 7/16/2009 4:03 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Umbrella Sampling

On Thu, Jul 16, 2009, Hemant Kumar wrote:

> I want to calculate free energy change during the process of insertion of
> a molecules inside a pore.So I am planning to to umbrella sampling by
> defining distance between COM of pore and molecules as the reaction
> coordinate.
> Now I am unable to figure out ,how to define this distance as my reaction
> coordinate in my input file(DISANG).To be more specific,I have problem in
> understaning iat(n) variable in &rst namelist.

To have a coordinate that is the center of geometry of several atoms, set
iat1<0 and use the igr1 to specify the atoms involved. See section 6.11.5
in the manual for an example of this.

Don't use too many atoms in igr1, or things may become unstable. You may have
to just use some selected atoms of the pore to compute its COM.


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Received on Thu Jul 16 2009 - 18:08:27 PDT
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