[gmx-users] Triclinic box output error

[Sevasteiadis, Michail]

Hi Tsjerk,

Thank you again for your replies.

I have found the line in the manual and probably we are talking about the same thing.
Something last that I have just observed, it happens that after the simulation some molecules of the crystal on the Y boundaries form new bonds with the other side molecules of the crystal. 
They appear to be close enough to form bonds, so could the reason for that be the gromacs or a suspicion I have that the box length on Y is slightly smaller than it should ?

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 14:24
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Triclinic box output error

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.
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