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