I do not see topology file in your archive.
2009/6/25 <[email protected]> > The input files for EM of the job are in the attachment. > > > > Thank you for your time! > > > ----- 原始邮件 ----- > 发件人：Vitaly V. Chaban <[email protected]> > 收件人：[email protected], [email protected] > 主题：Re: 回复：Re: 回复：[gmx-users] Re: How to freeze the atoms? > 日期：2009-6-24 19:10:19 > > > It's difficult to say anything definite about your problem based on the > provided information. If the effect is critical for your job you may send me > all the input files of your system and hopefully I will try to look at them > on these days. > > 2009/6/24 <[email protected]> > >> I checke the ndx file and the numbers of atoms in that file are the same >> as in the corresponding residues. >> >> The atoms only move in EM and they stay still during equilibrium process. >> I have not run MD yet. So I don't know whether the atoms will move or not >> during MD run. >> >> Thank you! >> >> >> ----- 原始邮件 ----- >> 发件人：Vitaly V. Chaban <[email protected]> >> 收件人：[email protected], [email protected] >> 主题：Re: 回复：[gmx-users] Re: How to freeze the atoms? >> 日期：2009-6-24 13:00:20 >> >> >> 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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