[gmx-users] H-Bond, regarding

[Justin Lemkul]

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

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

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
http://www.thelemkullab.com

==================================================