[gmx-users] Center of simulation box

zhenlong li zxl1000 at gmail.com
Wed Oct 26 19:08:31 CEST 2011

Dear all,

In my simulation, when the simulation box shrinks, the center of box always
shift towards the origin even if the center motion is set to removed every
I just wonder if there is an anticipated center position for a given
simulation box in gromacs. The box type is dodecahedron in my simulation.

My problem is how to make sure a group of atoms, such as proteins,  sit at
the center of the simulation box after the simulation box become stable.
Current, as the center of the box floats, it is very difficult to maintain
it by position restraint of the center group.

Thank you in advance for any suggestions!

with best wishes
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111026/3419ee46/attachment.html>

More information about the gromacs.org_gmx-users mailing list