[gmx-users] SHAKE and pbc=full

leafyoung81-group at yahoo.com leafyoung81-group at yahoo.com
Thu Sep 8 13:01:13 CEST 2005


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?


Yang Ye

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