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

Vitaly V. Chaban vvchaban at
Wed Jun 24 07:00:20 CEST 2009

I do not know such effect although work with the 'freeze' option for a
number of years in many gromacs versions.

Are you sure that the numbers of the atoms in your ndx file are the same as
in the corresponding residues? I suggest that you should look for a problem

Do the atoms move only when EM is performed or during MD run as well?

- Vitaly

2009/6/24 <toby10222224 at>

> Dear all
>        The CNT itself does not move. Only C and O in carbonyl groups move
> and the distance of movement is not large. As I wrote, Each carbonyl group
> (C and O ) is considered as a residue named "Car" and the group name of
> carbonyl in the ndx file is "Car", too. Is there anything wrong with the
> groups?
>        Is it possible that the frozen atoms move a short distance due to
> the strong electrostatic forces. C in the CNT has no charge, while atoms in
> carbonyl groups take charges.
>        Thank you for your time!
> ----- 原始邮件 -----
> 发件人:Vitaly V. Chaban <vvchaban at>
> 收件人:gmx-users at
> 主题:[gmx-users] Re: How to freeze the atoms?
> 日期:2009-6-23 18:04:35
> >
> > 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,vvchaban at
skype: vvchaban, mob.: +38-097-8259698
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