Re: [AMBER] How to change the coordinates of the system

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 15 Jul 2019 09:26:36 -0400

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
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