[gmx-users] Trajectory files in vmd
Justin A. Lemkul
jalemkul at vt.edu
Sat Sep 26 13:22:02 CEST 2009
Aditi Borkar wrote:
> Dear Rui,
> Thanx for the explanation. I did not know that VMD only calculates the
> secondary structure fort he first frame only. Is there an option to
> calculate the secondary structure (say in New cartoon representation)
> of all the frames in the trajectory?
You can use the Tcl interface to do it - the ssrecalc() function is designed for
that. Check out the VMD user's guide and their mailing list forum for how to
Even more quantitative, though, is to use do_dssp to get a plot of secondary
> On Thu, Sep 24, 2009 at 5:39 PM, J. Rui Rodrigues
> <joaquim.rodrigues at estg.ipleiria.pt> wrote:
>> 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,
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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