[gmx-users] Trajectory files in vmd

Aditi Borkar aditi.borkar at gmail.com
Thu Sep 24 07:21:04 CEST 2009

Dear All,

When I am loading the GROMACS trajectory in VMD, I cannot the
evolution of the protein structure with time.

When I am creating pdb files from the trajectory at different time
steps using the dump option, I do see changes in the protein structure
with time. My final structure after the MD simulation is also a lot
different that my start. However, when loading the trajectory, I do
not see a gradual/drastic transition from the starting to the final
conformation in VMD.

Please suggest where am I going wrong.

Thank you
Aditi Borkar,
Tata Institute of Fundamental Research,

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