[gmx-users] change in conformation

Shine A shine.a at iisertvm.ac.in
Fri Dec 14 04:44:42 CET 2012


        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

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