[gmx-users] on Umbrella Sampling

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 1 15:04:25 CEST 2012

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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