[gmx-users] Trajectory files in vmd

[Justin A. Lemkul]

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 
use it.

Even more quantitative, though, is to use do_dssp to get a plot of secondary 
structure evolution.

-Justin

> 
> 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.
>>
>> --Rui
>>
>>
>> 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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>>
>> --
>> Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)
>>
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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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