[gmx-users] Trajectory files in vmd

J. Rui Rodrigues joaquim.rodrigues at estg.ipleiria.pt
Thu Sep 24 14:09:59 CEST 2009

Dear Aditi,

What do you mean with "evolution of the protein structure"? Are you referring to
*secondary structure*? By default, VMD only calculates it for the first trajectory frame.


On Thu, 24 Sep 2009 10:51:04 +0530, Aditi Borkar wrote
> 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,
> Mumbai.
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