[gmx-users] my minimization structure looks like a messy box?

[Justin Lemkul]

On 12/13/17 11:41 AM, MD wrote:
> It looks like this
> https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD

That's classic PBC.

-Justin

> On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 12/13/17 11:02 AM, MD wrote:
>>
>>> Hi Gromacs folks,
>>> Any of you have experienced having a messy box looking gro file after
>>> em.mdp?
>>>
>> Probably http://www.gromacs.org/Documentation/Terminology/Periodic_
>> Boundary_Conditions but you'll have to define "messy" if that's not
>> what's going on.
>>
>> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
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-- 
==================================================

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.biochem.vt.edu/people/faculty/JustinLemkul.html

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