[gmx-users] conformational change

[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.Then I calculated the rmsd deviation and radius
of gyration, it not showing any characteristic deviation.Is water molecule
change the conformation of helix inside the barrel? Is it necessary to
delete all the water molecules inside the barrel before dynamics? then
how?