[gmx-users] Re: Mdrun interrupted using a triclinc box

Yinghong xieyh at hkusua.hku.hk
Tue Oct 11 02:31:44 CEST 2005

Dear Yang Ye:

The PBC I used is one particular tpye of cubic box, which cross-section is a rhombus instead of rectangle.
As we know, a hexagon can be divided into three rhombus, ok? We call it as unit cell, which is the box I employed. Normally, some distance is existing between solute molecule and box boundary in most simulations. But in my simulated box, the boudary is initially tangent to the solute, which means there is almost no distance between solute and box boundary. As you said, if your DNA exceed the boundary, one part will be in the right side, and the other will emergy in the left side. This is also the case I often encountered.
In my simulation, the solute is a nanotube, as the simulation, the tube will be outside the box and broken into several parts. And finally, the run will be stopped possibly due to the broken nanotube.

> but Gromacs told me that has no effect for unit cell representation.
which will be told when I use "trjconv -ur tric -pbc whole (not inbox)" to define a tric box.  Do you know how to define a tric box as I mentioned before?

Thanks for your help and discussion.

Xie Yinghong
Hong Kong University.

> 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.
What do you mean by "broken"? In my simulation, molecule will gradually
slide to the boundary of the box and even move out from it. But at long
as it is still kept at a good shape, there is no impact to MD
simulation. For DNA, there could be case that one strand on the left
boundary and another on the right boundary. A awk script or program will
do the trick and make analysis proceeding.

> And, if "-pbc whole" was adapted, the molecule could be kept intact,
> but Gromacs told me that has no effect for unit cell representation.
where did this "gromacs told me..." come from?

> 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.
Also, what do you mean "broken" here?

> 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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