[gmx-users] on Umbrella Sampling

Acoot Brett acootbrett at yahoo.com
Sun Apr 1 15:11:39 CEST 2012

I have not read your original article. Maybe I will read it tomorrow.  
But the original pdb file has 5 same chains, and from your tutorial it seems you pdb file for the tutorial has 2 different chains. Will you please let me know how do you get you pdb file for your tutorial/ Or you just have 1 chain in your tutorial PDB file, but in the gro file you defined it into 2 chains from a single chain?

 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, 1 April 2012 11:04 PM
Subject: Re: [gmx-users] on Umbrella Sampling

Acoot Brett wrote:
> Thanks.
>  The original PDB file (2BEG) has 5 chains. In your tutorial you fix chain B. Thus if I am right, the energy calculated should be the disintegation energy of the whole protein to the 5 chain peptide. In addition the protein chain in the original pdb is from residue 17 to 42.
>  This makes me confused when you define "1-27" to chain A, and "28-54" to chain B.
>  It seems your tutorial protein is a 2 chain protein, not the 5 chain protein.
>  Can you give me further clarification?

The .gro file is renumbered during pdb2gmx.


-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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