[gmx-users] Which kind of box?
rodrigoreston at yahoo.com.br
Thu Oct 13 15:53:41 CEST 2005
I'm not sure if your problem is this one... Have you
visualized what the triclinic shape looks like? If you
haven't, search for the word "triclinic" on Google
Images to see one and maybe then it'll help you design
the best approach to encase your system (by the way,
do that to the other shapes available in editconf).
Also, you might not need to specify the dimensions of
the triclinic box - perhaps, just using the option -d
and typing the distance (like [0.5] nm) from your
molecule to anyone of the triclinic box faces will do.
Rodrigo S. Reston, BSc.
--- Yinghong <xieyh at hkusua.hku.hk> wrote:
> 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
> Xie Yinghong
> Hong Kong University
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