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
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