[gmx-users] How to make all parts of a protein in the periodic box in when running "gmx editconf" command

[Bratin Kumar Das]

Hi ..
You didn't mentioned the box-type by -bt flag
You mention that...I hope your problem will be resolved.

On Thu 22 Aug, 2019, 7:24 PM sunyeping, <sunyeping at aliyun.com> wrote:

> Dear all,
>
> I run the"gmx editconf" command to make a periodic cubic box around my
> protein for adding water:
>
>   gmx editconf -f protein.gro -o newbox.gro -c -d 1.0
>
> Then I visualize the priodic box in VMD. I find that one end of my protein
> is out of the box (Please see the part in red circle in image at
> https://drive.google.com/file/d/1M6msh1UA0fOZ4GOuGJVlJHTOtHrzwh7u/view?usp=sharing).
> Even if I  increase the value of "-d" option to 1.5, this end of the
> protein is still out of the box. This will result in visualization problem
> of the MD trajectory. This part at one end of the molecule which is out of
> the box will jump to the other end of the molecule in VMD and pymol. Please
> see the part in the red circle in the image at (
> https://drive.google.com/file/d/1GAP4oS78nAB6p-ZhPmT9A-6ZZnohhkeq/view?usp=sharing).
> The is the image for em.gro the structure after energy minimization.  The
> trjconv command with -pbc cluster -center -ur cpmpact command cannot solve
> the problem.
>
> So could you tell me how to keep all part of the protein in the periodic
> box when running "gmx editconf" command? Thank you in advance.
>
> Yeping
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