[gmx-users] About Pulling code in Gromacs 5.0.2

[hang yin]

Hello all,

Recently, I preformed a SMD, pulling a nano diamond across the membrane. I
found that pull_geometry position in the Gromacs 4.6.5 (suggested in the
tips of the US tutorial by Justin.A ) was replaced by pulling with absolute
reference point in Gromacs 5.0.2. After defined pulling parameters
according to the manual, Gromacs gave me a warning that "This will lead to
artifacts". I really want to know what did it mean, so I ignored it by
using maxwarn 1 and saw what would happen. Finally I got a segment fault
that a bonded atom moved away, out of the cut-off distance.

Can you give me some advises? How can I treat the pulling correctly for
this penetrating process and why does the absolute reference lead to
artifacts.

Many thanks!

Hang