[gmx-users] SHAKE and pbc=full

[leafyoung81-group at yahoo.com]

Hi,

In my system, I constructed a rigid structure (quite
big, 110x110x50 A), any two of the atoms are bonded
and are converted to constraints using
constraints=all-bonds. I used SHAKE because LINCS
could not do so.

When doing MD with pbc=xyz, when part of the structure
moving outside the boundary, the atoms exploded. When
I switched to pbc=full, grompp gives me "can not do
full pbc with Shake, use Lincs".

Is there any work-around for this issue?

Thanks.

Yang Ye