[gmx-users] how to center the protein?

rama david ramadavidgroup at gmail.com
Mon Oct 8 11:46:18 CEST 2012


you can put the protein in center by adding flag -center to trjconv ( see
trjconv -h)

use the proper index file ( if you made ) -n ..

You can also use the -pbc cluster and extract the specific time frame by
flag  -dump

see trjconv very carefully ,It has  the way to do it.

With best wishes and regards
Rama david

On Mon, Oct 8, 2012 at 3:06 PM, Albert <mailmd2011 at gmail.com> wrote:

> Dear:
>   I am using the command:
> trjconv -f md.trr -s md.tpr -dump 54000 -o md.pdb -pbc mol
> trjconv -f md.pdb -s md.tpr -o fit.pdb -fit rot+rans
> to extract a frame of my md simulation and I found my protein is not in
> the centre of simulation box. here is a figure for it:
> https://dl.dropbox.com/u/**56271062/position.jpg<https://dl.dropbox.com/u/56271062/position.jpg>
> as we cab see the protein is just in the corner of box and the water
> molecules (lefft sphere) in the protein was separate from protein and on
> the otherside of box.
> Albert
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