[gmx-users] genconf and bonded interactions

[Fabio Affinito]

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.


-- 
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
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