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

[MD]

ah, that explains. thanks Justin!
Ming

On Wed, Dec 13, 2017 at 11:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>