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

Vitaly V. Chaban vvchaban at gmail.com
Tue Jun 23 12:04:35 CEST 2009

> 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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