Dear Zhanfeng,
it may be just a visualization problem, as Carlos suggested.
Is the visualization result of your system after initial top/crd
creation ok? After minimization/relaxation? After equilibration?
Do you have any 'special' molecules (i.e. non-peptides or ligands with
newly created parameters) in your system?
Is the visualization result the same, if you convert your top/rst files
into a pdb file via ambpdb?
(Did you use the right top files for visualization?)
Good luck!
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 03.07.2022 um 03:49 schrieb 王展峰 via AMBER:
> I check this. No matter whether autoimage the system or not, the trajectory is abnormal.
>
>
>> -----原始邮件-----
>> 发件人: "James Kress via AMBER" <amber.ambermd.org>
>> 发送时间: 2022-07-03 01:20:29 (星期日)
>> 收件人: "'AMBER Mailing List'" <amber.ambermd.org>
>> 抄送:
>> 主题: Re: [AMBER] atomic chaos in the equilibration trajectory
>>
>> Did you try to autoimage the system?
>>
>> -----Original Message-----
>> From: 王展峰 via AMBER <amber.ambermd.org>
>> Sent: Saturday, July 2, 2022 8:46 AM
>> To: Carlos Simmerling <carlos.simmerling.gmail.com>; AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] atomic chaos in the equilibration trajectory
>>
>> The energies are normal (see the attached energies figure).
>>
>>
>>> -----原始邮件-----
>>> 发件人: "Carlos Simmerling via AMBER" <amber.ambermd.org>
>>> 发送时间: 2022-07-02 20:39:37 (星期六)
>>> 收件人: "王展峰" <zfwang.bnu.edu.cn>, "AMBER Mailing List"
>>> <amber.ambermd.org>
>>> 抄送:
>>> 主题: Re: [AMBER] atomic chaos in the equilibration trajectory
>>>
>>> How are the energies? It may just be a visualization problem.
>>>
>>> On Sat, Jul 2, 2022, 8:28 AM 王展峰 via AMBER <amber.ambermd.org> wrote:
>>>
>>>> Dear Users,
>>>>
>>>>
>>>>
>>>>
>>>> I am runing an equilibration with CPU version pmemd. However, I
>>>> found the atoms are messy in the trajectory (see the figure 1
>>>> below). I tested it with GPU version. The trajectory is normal.
>>>> Besides, I also tested another system and same problem was found:
>>>> the trajectory is normal for GPU, yet not for CPU. The input
>>>> parameters was attached in Figure 2. Is it the problem of the input parameters?
>>>>
>>>>
>>>>
>>>>
>>>> Thanks for your help in advance.
>>>>
>>>>
>>>>
>>>>
>>>> Figure 1.
>>>>
>>>>
>>>>
>>>>
>>>> Figure 2.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Zhanfeng Wang_______________________________________________
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>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
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Received on Thu Aug 04 2022 - 13:34:08 PDT
