[gmx-users] genconf and bonded interactions

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 26 16:30:07 CEST 2011

Fabio Affinito wrote:
> 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..)

By whole, I mean that the molecules are not split across periodic boundaries in 
the initial configuration that you replicated.  If you replicate a periodic 
break, then you split the molecules by a distance equal to the new periodic 



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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