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

Mark Abraham mark.j.abraham at gmail.com
Wed Jan 28 12:50:55 CET 2015


Judicious use of the order of operations and perhaps not choosing the
System group are probably all you need here. Suggestions at


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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