There is no problem with your system. To have the same water thickness, you could move the membrane in the center of the box.
________________________________________
De : Maria Bzówka [m.bzowka.tunnelinggroup.pl]
Envoyé : lundi 15 juillet 2019 15:52
À : AMBER Mailing List
Objet : Re: [AMBER] How to change the coordinates of the system
Hi Dan,
Thank you for your suggestion, it works. However, the new problem showed
up. Right now, the water layers do not have the same thickness (you can
see in the attached file). I don't know what to think about it. Does it
mean that something is wrong with the equilibration itself?
Maria
pon., 15 lip 2019 o 15:26 Daniel Roe <daniel.r.roe.gmail.com> napisał(a):
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 15 2019 - 07:30:02 PDT
