[gmx-users] Re: How to freeze the atoms?

[Vitaly V. Chaban]

>
> 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!
>

All the atoms which relate to your frozen groups should be non-movable
during MD.

>the coordinates of C and O in carbonyl groups changed.

Only ones of CHO changed? And the CNT itself is nonmovable? Check your
groups please.


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698
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