toby10222...@sina.com wrote:
Dear all
I attach 8 carbonyl groups onto a carbon nanotube (CNT). Each
carbonyl group is considered as a residue named "Car" and each carbon
atom in the CNT is considered as a residue named "Gr1". In the mdp file,
the freezegrps are Gr1 and Car, and the freezedim are Y Y Y Y Y Y. Does
it mean that all the C in the CNT and C and O in the carbonyl groups are
fixed in three dimensions and they can not move in any direction.
However, when I made the energy minimization, the coordinates of C and O
in carbonyl groups changed.
How can I really fix the atoms? Look forward for your suggestions!
group names and residue names only mean the same thing if you've
constructed your groups accordingly.
Mark
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