[gmx-users] how to center the protein?
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
use the proper index file ( if you made ) -n ..
You can also use the -pbc cluster and extract the specific time frame by
see trjconv very carefully ,It has the way to do it.
With best wishes and regards
On Mon, Oct 8, 2012 at 3:06 PM, Albert <mailmd2011 at gmail.com> wrote:
> 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:
> 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.
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