[gmx-users] Triclinic box output error

[Tsjerk Wassenaar]

Hi Michail,

Ah, so you mean that the positions of the atoms changed. The box is exactly
the same. The reason for the reordering is that Gromacs puts the atoms in
the corresponding rectangular brick, which is more convenient
computationally. Check the section in the manual on PBC. It's explained
there.

Cheers,

Tsjerk

On Thu, Mar 5, 2015 at 3:14 PM, Sevasteiadis, Michail <
michail.sevasteiadis.14 at ucl.ac.uk> wrote:

> Hi Tsjerk,
>
> Thank you for your reply.
>
> Initial.gro :  13.81400  11.35913   3.31043   0.00000   0.00000   4.68932
>  0.00000   0.90944  -1.12273
> Final.gro   :  13.81400  11.35913   3.31043   0.00000   0.00000   4.68932
>  0.00000   0.90944  -1.12273
>
> Best Regards,
> Michail
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Tsjerk
> Wassenaar
> Sent: 05 March 2015 13:01
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Triclinic box output error
>
> Hi Michail,
>
> Can you post the box line (last line from .gro) before and after the
> simulation?
>
> Cheers,
>
> Tsjerk
>
> On Thu, Mar 5, 2015 at 12:46 PM, Sevasteiadis, Michail <
> michail.sevasteiadis.14 at ucl.ac.uk> wrote:
>
> > Hello,
> >
> > I run a short-time simulation of a liquid on a crystal surface using
> > triclinic box PBC but when it finishes it returns the Y side of the
> > crystal in right angle(like cutting it in right angle) while it
> > retains the X and Z angles. When checking the pbc box in VMD it's not
> > changed and shows half of the Y side out of the box. Any ideas?
> >
> > Thank you,
> > Michail
> > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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-- 
Tsjerk A. Wassenaar, Ph.D.