[gmx-users] Which kind of box?

Yinghong xieyh at hkusua.hku.hk
Fri Oct 14 04:20:13 CEST 2005

Dear users:

I am very strange with the concept of triclinic, so I need your instruction for the choice of my simulation box.

In my current system, the lengths of a b c are respectively 5.0, 5.0, 10.0nm, and the angles between bc, ac, ab are 90, 90  and 120 degrees. Because of my misunderstanding of triclinic, maybe, the following steps are somewhat wrong, can you help me to point them out?

1. editconf  -f mole.gro -o out.gro -bt tric -box 5 5 10 -angles 90 90 120 -c
Should I use the option "-bt tric" here? If not triclinic, possibly, "-bt tric" is wrong.

2. genbox -cp out -cs -p topol.top -o b4em.gro

3. grompp -v -f em -c b4em -p topol -o box.tpr

4.trjconv -f b4em.gro -s box.tpr -o b4em2.gro -ur tric -pbc inbox    ---- for visualization only.
What should my choice for options "-ur & -pbc" in this case?

Urgent equiry and any help will be  greatly apprieciated.

Xie Yinghong
Hong Kong University
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