Hi,
This is happening because autoimage is choosing a single molecule from
one of the bilayers as the anchor. After "autoimage", you could
'center' on the bilayer (i.e. use 'center' and select the entire
bilayer) and then image only water, ions with 'image bymol
:WAT,Na+,Cl-' etc.
Alternatively you could try to choose the end of one of the lipid
chains (near the bilayer center) as the anchor instead of an entire
lipid.
Hope this helps,
-Dan
On Mon, Jul 15, 2019 at 9:53 AM Maria Bzówka <m.bzowka.tunnelinggroup.pl> wrote:
>
> 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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Received on Mon Jul 15 2019 - 08:00:02 PDT
