[gmx-users] trjconv for hexa-meric protein

Tomoshi Kameda kameda-tomoshi at aist.go.jp
Wed Sep 6 12:33:15 CEST 2006


I simulate a hexa-meric protein (443*6=2658 residues with about 90000
water) Especially, I'm interested in water behavior around the protein.

The 1ns simulation is finished normally, but trjconv produces abnormal
structure. For example, the protein go outside my waterbox, water
molecules are diverse abnormally...etc.

I try various options:

trjconv -s full.tpr -f full.trr -o full.xtc -pbc nojump
trjconv -s full.tpr -f full.trr -o full.xtc -pbc cluster
trjconv -s full.tpr -f full.trr -o full.xtc -fit rot (select 1(thus
protein) for fitting group)

And, I watch full.xtc using VMD, but they are strange in all cases.
For your information, I use cubic periodic boundary condition.

Please suggest me. Greetings,


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