Gromacs: How Do I Move A Box?

Question

[Adobe]

I've made a simulation with a periodic boundary conditions - but lipid bilayer got assembled in such a way - that water (which is not shown in the picture below) stacked in the center of the box:

How do I move the box - so to make bilayer look more like a bilayer - in my cell-box?

Edit:

A warm thanks goes to comcon1.

In case one doesn't remember - one can find a box size by

gmxdump -f traj.trr | less

or

gmxdump -f traj.trr | vim -

to browse it in vim.

It said me that the initial box size was 7.5 7.5 7.5

So I've made a script to run through a range of x values (you must have confout.gro and topol.tpr files in the dir):

#!/usr/bin/python2.7

from numpy import arange
from os import system

for i in arange(-1.05, 5.05, 0.1):
    system("editconf -f confout.gro -translate %g 0 0 -o edtOut%g.gro" %(i, i))
    system("echo 0 | trjconv -f edtOut%g.gro -trans %g 0 0 -pbc res -o trjOut%g.gro" %(i, i, i))

This way I found that the bilayer is alright after the translations ranging from 0.05 to 3.25. So I've choosen 1.65 as a middle value. Than I've moved trajectory by:

echo 0 | trjconv -o trjOut1.65.trr -trans 1.65 0 0 -pbc res

To rotate a gro file - one should also first -rotate it with editconf, and then trjconv it with -pbc res:

editconf -f confout.gro -rotate 0 90 0 -o  edtOut.gro
echo 0 | trjconv -f edtOut.gro -pbc res -o trjOut.gro

Of cource one can combine rotate and translate in the same shot.

It looks like there's no utility written to rotate trajectory trr file.

[Neilfws]

This is a very specialist question. Have you tried the Gromacs mailing list? - http://www.gromacs.org/Support

[Adobe]

I went on to write a PyMOL script (here) - which translates the structure (either gro or pdb) to a given vector and generates the picture. Typical usage: bk-pymol-pic.py -f confout.gro -s "resi 1-128" -x "-2" -y "-3" -z "0".

Answer 1

[Comcon1]

You can simply translate your system with editconf -translate x y z. You need to use x=boxx/2. It makes the system with one half will be in the periodic box and other half - out of periodic box. Then use 'trjconv -f .gro -o .gro -pbc res'. This command collects all residues into the box keeping residues uncut.

[Keith Callenberg]

@Adobe: I don't know the real answer, but one way to get an idea is to go into Graphics > Representations, then go to the Periodic tab and and some extra periodic images by checking the boxes. This will give you a good indication as long as there are molecules near the edges of the box.

[Greg P]

To show the box boundaries in VMD, go into the VMD command line and type 'pbc box'

[Adobe]

By the way - how can one display the periodic box boundaries in VMD?

[Adobe]

@Greg P: thanks - it works!

[Adobe]

And in PyMOL it is show cell.