Hi,
'autoimage origin' will center the system at the coordinate origin
(bottom corner of the box). Just omit the 'origin' keyword from the
autoimage command and remove the subsequent center/image commands.
Hope this helps,
-Dan
On Mon, Jul 15, 2019 at 7:32 AM Maria Bzówka <m.bzowka.tunnelinggroup.pl> wrote:
>
> Hi all,
>
> I work with the system which consists of 128 lipids bilayer and water
> molecules. I used the cpptraj to center the whole system using following
> commands:
>
> trajin step6.1_equilibration.nc
> trajin step6.2_equilibration.nc
> trajin step6.3_equilibration.nc
> trajin step6.4_equilibration.nc
> trajin step6.5_equilibration.nc
> trajin step6.6_equilibration.nc
> autoimage origin
> center :1-128 mass origin
> image origin center familiar
>
> In VMD the system itself looks fine, but when I wanted to check the pbc
> box, it only partially overlaps with the system (you can see in the
> attached file).
> Should I somehow change the cpptraj commands?
>
> Thank you in advance for suggestions
>
> Maria
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Received on Mon Jul 15 2019 - 06:30:05 PDT
