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

[Vitaly V. Chaban]

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 <toby10222224 at sina.com>

> 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 <vvchaban at gmail.com>
> 收件人：toby10222224 at sina.com, gmx-users at gromacs.org
> 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 <toby10222224 at sina.com>
>
>> 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 gmail.com>
>> 收件人：gmx-users at gromacs.org
>> 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 univer.kharkov.ua,vvchaban at gmail.com
> skype: vvchaban, mob.: +38-097-8259698
>
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