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 there. Do the atoms move only when EM is performed or during MD run as well? - Vitaly 2009/6/24 <[email protected]> > 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 <[email protected]> > 收件人：[email protected] > 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: [email protected],[email protected] skype: vvchaban, mob.: +38-097-8259698
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