[gmx-users] getting rid of PBC, completely

Chandan Choudhury iitdckc at gmail.com
Thu Jan 19 07:39:39 CET 2012

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 (

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

#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

#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.


Chandan kumar Choudhury
NCL, Pune
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