[gmx-users] How to freeze the atoms?

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 23 11:09:59 CEST 2009

toby10222224 at 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.


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