AMBER Archive (2009)

Subject: RE: [AMBER] Umbrella Sampling

From: Hemant Kumar (hemant_at_physics.iisc.ernet.in)
Date: Sat Jul 18 2009 - 14:28:19 CDT

Thaks Matt & Dr. case , I am able to do it now

With regrads,
Hemant Kumar
Graduate Student
CCMT,Department of Physics
IISC,Bangalore
URL www.physics.iisc.ernet.in/~hemant

On Thu, 16 Jul 2009, Seetin, Matthew wrote:

> 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: amber-bounces_at_ambermd.org 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.
>
> ....dac
>
>
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