[gmx-users] trjconv centre protein

[Justin Lemkul]

On 3/19/13 7:44 AM, Ewaru wrote:
> Hi,
>
> I know this question has been asked for a few times already but I don't seem
> to get it. :(
> I did:
>
> 1) editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt dodecahedron
> 2) genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top
> 3) grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
>
> and then I view the solv.gro file in VMD and found out that the protein is
> hanging out from the box as in the attached image:
>
> http://postimage.org/image/6df12u991/
>
> I tried to put it in the centre with the command:
>
> 4) trjconv -s ions.tpr -f solv.gro -o solvcentre.gro -pbc mol -ur compact
>
> But it shows that the protein (solvcentre.gro) is still the same (hanging
> out from the box). Did I overlook something? Can I proceed with EM?
>

There is no "outside" of a periodic box.  The system is infinite, so you can of 
course proceed with EM.  If you want to center the protein, I would suggest 
using the -center option of trjconv to your command #4 above; that's what it does.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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