[gmx-users] about truncated octahedral periodic box

Yang Ye leafyoung at yahoo.com
Wed Jul 4 03:53:23 CEST 2007

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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