[gmx-users] H-Bond, regarding

Justin Lemkul jalemkul at vt.edu
Thu May 3 14:13:58 CEST 2018

On 5/3/18 2:21 AM, RAHUL SURESH wrote:
> Hi all
> I have performed MD simulation of a dimer [ Chain A and Chain B]. I want to
> calculate the interaction between both the chain [ Vdw, Electrostatics].

Separating interaction energies this way is unphysical. See recent 
discussion on this list on this topic.

> Also, I want to calculate H-Bond between these two chains. How should I set
> the Index file?

Make an index group for each chain, either by chain ID (if you have a 
.pdb or .tpr that preserved the chain ID) or by residue number (in any 
type of coordinate file).



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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