<br clear="all">Dear gmx-users,<div><br></div><div>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 (<a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a>). </div>
<div><br></div><div>Below are my executed commands : </div>
<div><br></div><div># Made the system whole</div><div><br></div><div>echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc</div><div><br></div><div># 0 is the whole system. md0-4.tpr is the initial tpr file containing whole (no broken) polymer inside the cubic box.</div>
<div># Extracted 1st frame from the initial trajectory</div><div><br></div><div>echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump 0</div><div><br></div><div># used the whole trajectory to remove jumps with reference to the 1st frame.</div>
<div>echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o 0-4_nojump.xtc</div><div><br></div><div>#system is being centered</div><div>echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc -center</div>
<div><br></div><div>#putting every atom in the box</div><div>echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom</div><div><br></div><div>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.</div>
<div><br></div><div>Chadan</div><div><br></div><div>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
</div>