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

[Li, Shi]

>
> Message: 3
> Date: Thu, 22 Aug 2019 21:53:25 +0800
> From: "sunyeping" <sunyeping at aliyun.com>
> To: "gromacs.org_gmx-users"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] How to make all parts of a protein in the
>         periodic box in when running "gmx editconf" command
> Message-ID:
>         <0c07c92c-a134-4057-a8a2-13a1143ae486.sunyeping at aliyun.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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.
>
> Have you tired the -pbc nojump flag see if that can give you a different
representation of the structure?

Shi

> 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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> End of gromacs.org_gmx-users Digest, Vol 184, Issue 58
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