[gmx-users] PBC correction to visualize a protein-membrane structure

[Mark Abraham]

On May 16, 2014 7:03 PM, "Juan Munoz-Garcia" <
juan.munoz-garcia at bioch.ox.ac.uk> wrote:
>
> Dear Justin,
>
> thank you. I’ve tried the following but neither of them worked, I get the
same result.
>
> trjconv -f input.gro -o output.gro -s .tpr -trans 0 0  z_box/2 -pbc mol
-ur compact
>
> trjconv -f input.gro -o output.gro -s tpr -trans x_box/2  y_box/2
 z_box/2 -pbc mol -ur compact

You need to use numbers.

Mark

>
> This is the last line of my input.gro file
>
> 19.51671  19.51671  13.80040   0.00000   0.00000   0.00000   0.00000
9.75836   9.75836
>
> Juan C.
>
>
> Your system was probably centered at z=0 instead of z = z_box/2 (commands
used
> for building the system would also help - I guess I should have been more
> clear), hence it's getting split across PBC.  trjconv -trans in
conjunction with
> -pbc mol should be what you need.
>
> -Justin
>
> --
>
> Begin forwarded message:
>
> From: Juan Carlos Munoz Garcia <juan.munoz-garcia at bioch.ox.ac.uk<mailto:
juan.munoz-garcia at bioch.ox.ac.uk>>
> Subject: Re: PBC correction to visualize a protein-membrane structure
> Date: 16 May 2014 14:08:50 BST
> To: <gromacs.org_gmx-users at maillist.sys.kth.se<mailto:
gromacs.org_gmx-users at maillist.sys.kth.se>>
>
> Thank you Justin,
>
> please find a dropbox link to the image below.
>
> I’ve used
>
> trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
> trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact
-center
>
> and different combinations of those
>
>
https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png
>
> Thank you.
> Regards.
> Juan C.
>
>
> --
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