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?
On Thu, Sep 24, 2009 at 5:39 PM, J. Rui Rodrigues <joaquim.rodrig...@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. >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aditi Borkar, Tata Institute of Fundamental Research, Mumbai. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
