[gmx-users] genconf and bonded interactions

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 26 16:38:12 CEST 2011

Fabio Affinito wrote:
> On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
>> 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 distance.
>> -Justin
> Ok, so: no, it's not broken.

What you need to do is use the information mdrun provided you to diagnose what's 
going on.  Apparently atoms 193657 193660 are separated by 31 nm.  What are your 
box vectors?  Where are these atoms in the system?  Then you'll have your 
answer.  The only reason I can think of for such extreme distances is a 
periodicity issue.



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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