[gmx-users] Mdrun interrupted using a triclinc box

Yinghong xieyh at hkusua.hku.hk
Fri Oct 7 22:05:54 CEST 2005

Dear users:

In my system, I chose a triclinc box (monoclinic cell) as my periodic boundary condition, which is defined as follows:

editconf -f *.pdb -o -bt tric -box 5 5 10 -angles 90 90 120 -c
genbox -cp out -cs -p topol -o b4em
grompp -v -f em -c b4em -p topol -o box
trjconv -f b4em -s box -o b4em2.gro -ur tric -pbc inbox 

If I used "-pbc inbox", my simulated molecule would be broken. And, if "-pbc whole" was adapted, the molecule could be kept intact, but Gromacs told me that has no effect for unit cell representation.

In my simulations, I empolyed "-pbc whole" in order to keep molecule intact, but after ~200ps simulation, mdrun is interrupted, and the initial intact molecule is also broken at this moment. 

So, Could you tell me that the way I defined a triclinc box (not hexagonal box) is right? 
Which option should I choose in "trjconv" for -ur and -pbc?
What made my simulation stopped?

Because this is my first time using triclinc box, many things are very strange for me. 
Any help is appreciated.

Xie Yinghong
Hong Kong University
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