Dear Justin, Thanks, sure I will give more details.
This command I've used for trajectory conversion: trjconv -pbc mol -center -s protein.tpr -f old.trr -o new.trr Then I was analysing a new and old trajectory in VMD with my own script. I have noticed that in old trajectory water234 between frame 0 and 1 moves 1.2089872880760837 A, whereas the same water molecule between the same frames but in the new trajectory moves 1.4933788404331632 A I check different water - water236 and situation was similar: old trajectory -> 0.6436778227352694 A and in new trajectory it was 0.2921395545132566 A So after trajectory conversion water displacement is different, sometimes in the new trajectory is bigger and sometimes is smaller that it was in old one... I used the same conversion for part of my simulation where protein was in the center of the system, and results were similar. I believe is not problem with my vmd script because even when I open in the same window new and old trajectory in VMD I can see "by eye" the difference of water movement.... I am missing something? Thanks for any suggestions and help! Best! tomek On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Tomek Wlodarski wrote: >> >> Hi all! >> >> I have a trajectory of simulation (protein in box of water) and I >> would like to have all the time protein in the center of the water >> box, becasue protein is drifting to the edge during simulation and I >> am calculating some properties of water arround the protein. >> I was playing with trjconv and -pbc and -center options and I menage >> to do what I wanted, however there was something bizarre for me or >> maybe I do not fully understand how this centering works.... >> I noticed that the same water molecule traverse different distance >> between the same frames of simulation in the original than in >> converted trajectory... >> Why and how it is possible? >> Thank you for any suggestions and help! > > Without seeing the exact command(s) you used to produce the centered > trajectory, especially if it was a combination of some -pbc method and > -center, then it's impossible to say for certain. I'd venture a guess that > you've simply managed to "correct" for water molecules jumping across > boundaries or something, but that's just a guess, and without actual > commands and the output you are obtaining, there's not much more to offer > beyond speculation. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- 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
