On 19/01/2012 5:39 PM, Chandan Choudhury 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.
You can't "get rid of PBC", you can only manage it. The question reduces
what you want to see if a molecule diffuses across the periodic boundary
from near one end of the polymer to the other end.
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
So here you said "let molecules diffuse away from the solute".
#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
... and now you said "take all the atoms and put them back in the box",
creating jumps whenever one crosses the boundaries.
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.
Don't simulate with them :-P Is your analysis technique sound for the
periodic case?
Mark
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