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

nazli kashani javid nazlikjavid at gmail.com
Wed Jan 28 10:04:29 CET 2015

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)


after centering, my protein got back to the box but it lost its pack
 so I tried trjconv command again :

trjconv -f a.xtc  -o b.xtc -s md.tpr -pbc nojump

(please see: afternojump.jpg)


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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