[gmx-users] genconf and bonded interactions

Fabio Affinito f.affinito at cineca.it
Tue Jul 26 16:28:17 CEST 2011

On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:

> Were the molecules whole in the coordinate file you replicated? If not,
> the bonds will now be assigned across the entire box.
> -Justin
Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)


Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198

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