Hi,
The two systems before and after imaging are equivalent given periodic
boundary conditions. The fact that you get the same distances before
and after imaging shows this. If you google e.g. 'amber periodic
boundary conditions' you get many more in-depth explanations (such as
http://archive.ambermd.org/201307/0308.html).
For QM you likely want the "autoimaged" coordinates.
-Dan
On Fri, May 5, 2017 at 3:45 AM, 鲁俊波 <lujb15.mails.tsinghua.edu.cn> wrote:
> Dear Daniel,
> I have calculated the distance between the NO3 and metal ion. The attached file am_cro_1.pdb is the structure with no periodic. The am_cro_2.pdb is the imaged structure. I use "distance" command to calculate the distance. But I find that the distances between metal ion and NO3 are same for two different structure. For structure 1, the distances are 3.5404, 3.4385, 3.4468. And for structure 2, the distances are 3.5406, 3.4385, 3.4477. They are nearly same. So I think the "distance" command also use the periodic condition of box.
> But I just calculate the distance between the N atom and metal ion by myself. I find there is largest distance, as we can see from the structure. The other two are same for both 2 structures.
> With my best regards,
> Junbo
>
>
>> -----原始邮件-----
>> 发件人: "Daniel Roe" <daniel.r.roe.gmail.com>
>> 发送时间: 2017-05-04 23:49:53 (星期四)
>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>> 抄送:
>> 主题: Re: [AMBER] The problem for image tool in AMBER
>>
>> Hi,
>>
>> First, 'autoimage' is usually a better command for re-imaging your trajectory.
>>
>> Second, when you have periodic boundary conditions you have to think
>> in terms of cell periodicity. For example, if in your first structure
>> (with apparently only 2 NO3- coordinating with your metal) the metal
>> ion is near a unit cell boundary, you could have a third NO3- nearby
>> that has been translated due to imaging. If after imaging you have 3
>> NO3- near the metal, this is probably what happened. You can also
>> calculate the distance of each NO3- to the metal to verify - the
>> 'distance' command will use the minimum imaged distance.
>>
>> -Dan
>>
>>
>> On Wed, May 3, 2017 at 11:20 PM, 鲁俊波 <lujb15.mails.tsinghua.edu.cn> wrote:
>> > Dear all:
>> > I have done a molecular dynamics. But I encounter a problem when I see the structure. The attached file am_cro_md.rst is my last structure of molecular dynamics trajectory, and md.in and am_cro.prmtop are the control and top files. I convert the structure to the pdb file using cpptraj:
>> > trajin am_cro_md.rst
>> > trajout am_cro_md1.pdb
>> > This structure seems no periodic. So I use the image tool:
>> > trajin am_cro_md.rst
>> > image center
>> > trajout am_cro_md2.pdb
>> > This two structures are different. The metal ion coordinates with two NO3- for first structure, but with three NO3- for second structure.They are so strange. I want to choose some solvent to do QM/MM optimization. So I do not know choose which structure. Is there something wrong? Can anyone give me a help?
>> > With my best regards,
>> > Junbo
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri May 05 2017 - 06:30:04 PDT
