[gmx-users] image centering

[Myunggi Yi]

Thank you for the reply.

I did center only, but I didn't see much difference from the original
structure.
Since the solvent is separated, centering cannot do much.

I decided to translate the whole system to shift up (out of box),
and then to move it back to the unit cell.
However, this "shift" doesn't work at all.
The output is exactly same as the original.

I may need the "framenr".

 -shift vector  0 0 0  All coordinates will be shifted by framenr*shift

This "help" message doesn't help me at all. I have no idea.

I changed my mind.
Since the "center" option gives me the translated structure,
I picked an atom to shift the system.

Now I can move the atoms outside box to the unit cell using -pbc option,
however, all options give me the broken molecules.

How can I solve this problem?

Happy holidays.


On Dec 26, 2007 5:40 AM, Alan Dodd <anoddlad at yahoo.com> wrote:

> Have you tried running trjconv with -centre (selecting SOL, obviously),
> and then running trjconv -pbc on the result?  I have a vague memory of
> finding seperating the commands gives a different result, as if the two
> options were interfering with each other.  What does the output look like
> when you use the option -centre?  If nothing else, seperating the commands
> might help you find the source of the problem.
>
> ----- Original Message ----
> From: Myunggi Yi <myunggi at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, December 25, 2007 9:48:29 PM
> Subject: [gmx-users] image centering
>
> Dear users,
>
> I have a membrane simulation trajectory,
> in which the solvent (water and ions) is separated by lipid bilayer.
>
> I want to center the solvent so that the membrane is separated by two
> layers at the bottom and top in the unit cell.
>
> I have tried the followings.
>
> trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -n ../memb.ndx -pbc cluster
> trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -s ../Eq9/eq9.gro -n ../memb.ndx
> -center rect -pbc whole
>
> Both pbc and center didn't work.
> Is there any way to center the solvent?
>
> Happy holidays.
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi>
>
>
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-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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