[gmx-users] Mdrun interrupted using a triclinc box

Yang Ye leafyoung81-group at yahoo.com
Fri Oct 7 21:13:08 CEST 2005

Yinghong wrote:

> 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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