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

Dilip H N cy16f01.dilip at nitk.edu.in
Mon Dec 18 08:54:34 CET 2017


Hello,
You need to use -pbc mol in your command for viewing the trajectory, then
this issue will be solved.



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On Wed, Dec 13, 2017 at 11:23 PM, MD <refmac5 at gmail.com> wrote:

> 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
> >>>
> >>> ==================================================
> >>>
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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
> >
> > ==================================================
> >
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student


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