Hi, I have two questions.
I have performed a simulation on my protein structure and after the simulation, I used trjconv to obtain snapshots after every 10 ns with the following command: trjconv -f md.xtc -s md.tpr -b 10000 -e 10001 -o md_10.pdb and chose 0 (system) for the group. However, when I see the same structure in PyMol as cartoon representation, I see the protein structure and few of the residues scattered elsewhere of a particular chain, say chain A. I am concerned whether my residues of that particular chain fragmented during simulation or is my way of obtaining snapshots wrong? Also, there was another question, I wanted to know how the geometry is preserved in the average structure as computed by gromacs?The average structure calculated during analysis would be the average of all the atomic positions/co-ordinates during the length of simulation. But, I wanted to know how are the bond angles treated for computation of the average structure? Since, we use the structure for further analysis too. Are the bond lengths distorted or they are retained while average is being computed? Also, what are the co-ordinates used for this computation? I would be really grateful if you could kindly guide me towards these queries. Kind regards -- Ankita Naithani -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
