[gmx-users] change in conformation

[Shine A]

Sir,

        I am studying the dynamics of a beta barrel shaped membrane
protein. The starting end of the barrel is a helix which is inside the
barrel. During salvation with genbox some water molecules entered inside
the barrel.Then I did the 20 ns dynamics.After dynamics more number of
water molecules trapped inside the barrel. I convert the output gro file
into pdb and viewed using pymol. Then I noticed that the starting helix
part is changed in to loop.what can I do to avoid this conformational
change?