Hi Chadan, You should stop after your second step, removing jumps. Don't center. And definitely don't put the system in the box, as that exactly undoes removal of jumps.
Cheers, Tsjerk On Thu, Jan 19, 2012 at 7:39 AM, Chandan Choudhury <iitd...@gmail.com> wrote: > > Dear gmx-users, > > I have a simulated a system containing a linear polymer in a cubic box with > water molecules. I need to get rid of PBC effect on the system such that I > can execute my own analysis code. I intend to compute the msd of water > molecules along the polymer backbone. So, when I execute my own analysis > code, I see the msd's are abrupt (i.e very high), this is due to the pbc. > So, for getting rid of PBC effect, I performed the suggested trjconv > workflow > (http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions). > > Below are my executed commands : > > # Made the system whole > > echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc > > # 0 is the whole system. md0-4.tpr is the initial tpr file containing whole > (no broken) polymer inside the cubic box. > # Extracted 1st frame from the initial trajectory > > echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump > 0 > > # used the whole trajectory to remove jumps with reference to the 1st frame. > echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o > 0-4_nojump.xtc > > #system is being centered > echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc > -center > > #putting every atom in the box > echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom > > Still when I execute my analysis code, I do see the abrupt behaviour in the > msd plot. Can someone guide me how to completely get rid of PBC artifacts. > > Chadan > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > -- > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
