[gmx-users] problem in centering of my protein in the box

[Mark Abraham]

Hi,

Judicious use of the order of operations and perhaps not choosing the
System group are probably all you need here. Suggestions at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Wed, Jan 28, 2015 at 10:04 AM, nazli kashani javid <nazlikjavid at gmail.com
> wrote:

> Dear all
>
> I study on simulation of kind of  protein, my system is 4-helix bundle
> protein which solves in the cubic water box. after my system
> was equilibrated, I ran 10 ns simulation without any position restraint.
> When I watched the trajectory file by VMD at the end of simulation, I
> realized some part of my protein went out of my box, but the protein kept
> its structure (4 alpha helix were compact).
> I used trajconv command to centerized my protein in the box:
>
> trjconv -f md.xtc  -o a.xtc -s md.tpr -center
>
> (please see: centering.jpg and centeringwithoutwater.jpg)
>
>
> https://www.dropbox.com/s/gel7vse0v7k3rf3/centering%20without%20water.jpg?dl=0
> https://www.dropbox.com/s/4ajvgnn0n9dnm1e/centering.jpg?dl=0
>
> after centering, my protein got back to the box but it lost its pack
> structure,
>  so I tried trjconv command again :
>
> trjconv -f a.xtc  -o b.xtc -s md.tpr -pbc nojump
>
> (please see: afternojump.jpg)
>
> https://www.dropbox.com/s/f1fzfcgerqbdq0u/after%20nojump.jpg?dl=0
>
> but it didn't work either.my protein's structure reassembled as the initial
> shape, while the water molecules, went out of the box surprisingly.
>
> how can I solve my problem? how can I retain my protein in the center of
> the box without  any changes in the structure and solvent system.
>
>  any help is appreciated.
>
>   thank you
> --
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