[gmx-users] about truncated octahedral periodic box

Rui Li moonfine at mail.sdu.edu.cn
Wed Jul 4 04:12:17 CEST 2007

Hi Yangye and Tsjerk,

Thank you for your reply.

I have used -c to center the molecule.

So it just seem to uncenter in visualizer. However, it will not influence the MD,

>From: Yang Ye <leafyoung at yahoo.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] about truncated octahedral periodic box
>Date:Wed, 04 Jul 2007 09:53:23 +0800
>On 7/3/2007 9:11 PM, Tsjerk Wassenaar wrote:
> > Hi Yang Ye,
> >
> > It was a different question; the question Rui Li asked was "why is my
> > protein not in the center of my truncated octahedron"?.
> >
> > The answer to that question is not:
> >> You shall use trjconv -ur compact -pbc atom to transform your model.
> > but is more fundamentally related to understanding the principles of
> > periodic boundary conditions (rather than to the use of trjconv).
> Thanks for the note, Tsjerk.
> There could be several possible reasons:
> The first reason could be that  Li didn't run trjconv -ur compact. What 
> is visible in any visualizer is a cuboid with protein not in the center. 
> This while can be solved technically, is actually related how non-cubic 
> box type is represented in gromacs.
> The second reason could be when specifying the box type with editconf, 
> molecule is not centered with -c. And Li actually used trjconv -ur 
> compact to convert the molecule before visualizing it.
> All in all, it is a very good practice to visualize the system before 
> running it.
> >
> >> This is my second time in the week answering this question.
> > I know.., I get the same feeling now and then.., but keep keen on
> > reading the question asked.
> >
> > Cheers,
> >
> > Tsjerk
> >
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