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Dear all<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I attach 8 carbonyl groups onto a carbon nanotube (CNT). Each carbonyl group is considered as a residue named "Car" and each carbon atom&nbsp;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.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; How can I really fix the atoms? Look forward for your suggestions!<br>
</blockquote><div><br>All the atoms which relate to your frozen groups should be non-movable during MD.<br></div></div><br clear="all">>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 groups please.<br>
<br><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>