I do not know such effect although work with the 'freeze' option for a number of years in many gromacs versions.<br><br>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.<br>
<br>Do the atoms move only when EM is performed or during MD run as well?<br><br>- Vitaly<br><br><br><div class="gmail_quote">2009/6/24 <span dir="ltr"><<a href="mailto:toby10222224@sina.com">toby10222224@sina.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><p>Dear all</p>
<p> 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?</p>
<p> 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.</p>
<p> Thank you for your time!</p>
<p><br>----- 原始邮件 -----<br>发件人：Vitaly V. Chaban <<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>><br>收件人：<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
主题：[gmx-users] Re: How to freeze the atoms?<br>日期：2009-6-23 18:04:35<br><br>><br>> Dear all<br>> I attach 8 carbonyl groups onto a<br>> carbon nanotube (CNT). Each carbonyl group is considered as a residue named<br>
> "Car" and each carbon atom in the CNT is considered as a residue named<br>> "Gr1". In the mdp file, the freezegrps are Gr1 and Car, and the freezedim<br>> are Y Y Y Y Y Y. Does it mean that all the C in the CNT and C and O in the<br>
> carbonyl groups are fixed in three dimensions and they can not move in any<br>> direction. However, when I made the energy minimization, the coordinates of<br>> C and O in carbonyl groups changed.<br>> How can I really fix the atoms? Look forward<br>
> for your suggestions!<br>><br><br>All the atoms which relate to your frozen groups should be non-movable<br>during MD.<br><br>>the coordinates of C and O in carbonyl groups changed.<br><br>Only ones of CHO changed? And the CNT itself is nonmovable? Check your<br>
groups please.<br></p></blockquote></div><br clear="all"><br>-- <br>Vitaly V. Chaban, Ph.D. (ABD)<br>School of Chemistry<br>V.N. Karazin Kharkiv National University<br>Svoboda sq.,4, Kharkiv 61077, Ukraine<br>email: <a href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a>,<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a><br>
skype: vvchaban, mob.: +38-097-8259698 <br>