Thank You very much :) Regards Suniba
On Fri, Feb 5, 2016 at 4:00 AM, Björn Sommer <bjo...@cellmicrocosmos.org> wrote: > Hello Everyone >> I have performed a md simulation if protein in water for 10ns and frames >> were obtained after every 10ps. I wanted to visualize the.gro and >> trajectory file in VMD, without water, so I prepared an index file >> containing protein only. Using editcon i removed water from md.gro as well >> but I loaded the files in VMD, 1000 time frames are loaded but I cannot see >> any change in structure or per frame conformation. The protein is still. I >> am not clear what to do. I tried keeping water in .trr and then in .gro and >> repeated steps but no results. When I use original .trr and .gro, only then >> i visualize the change in structure. Please help me >> >> Regards >> Suniba >> > Hi Suniba, > > sorry, but this is not the way how you should use VMD! It is much more > comfortable. > > You first import the PDB file, then you import the TRR or XTC file (make > sure that the actual PDB file is selected during loading, so that the > trajectory is associated with it). You may also first make the following > settings after importing the PDB, and then afterwards import the > trajectory. This might save time during loading and memory resources. > > Okay, you open now the representations window (Graphics -> > Representations). > > In the Representations window, select the tab "Selections". In the keyword > section, select "resname". Now, you will see in the field value all Residue > IDs contained in your PDB file. Use this IDs now in the selection. > > For example, water has often the name SOL or WAT etc. If you want to see > only the water, type in into the "Selected Atoms" section > > resname SOL > > If you want to see everything else, not the water, and also not the ions, > which could have the name NA, you say > > not resname SOL NA > > You want to see only the P atoms of DPPE with the resname DPE > > (resname DPE) and (name P8') > > Please note that, to select single molecules, you should have a look to > the original PDB file and check what the names of the atoms for the > corresponding molecule look like. > > To change now the representations, you find all options in the "Draw > stlye" tab. > > Now you want to have different representations for different atoms: just > click on "Create Rep". The last representation is duplicated, and you can > change it now. By double clicking on the entry in the list, you can hidea > an entry. > > Have fun! > Bjorn > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
