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

[Vitaly V. Chaban]

I do not see topology file in your archive.


2009/6/25 <toby10222224 at sina.com>

> 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 <vvchaban at gmail.com>
> 收件人：toby10222224 at sina.com, gmx-users at gromacs.org
> 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 <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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