[gmx-users] inquiring for solving trjconv problems

Mehdi Bagherpour mbagherpour7749 at gmail.com
Sat Jan 19 23:21:06 CET 2013

hello everybody

I have simulated DNA using CHARMM force field for 50 ns with 2 ps snapshots
for each step.
when I wanted to convert .xtc trajectory files to .pdb using trjconv,  some
of the snapshots were collaborated.
I have used periodic boundary conditions in this simulations.
To convert, I used bellow command:

trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center

In collaborated .pdb files two strands of DNA separated from each other.
when I used bellow command instead of above command, this collaborated .pdb
file will be corrected,
but some of the other .pdb files will be ruined as same as

trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol

would you please help me to solve this technical problem?

I am looking forward hearing of you,

Mehdi Bagher Poor

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