Hi, Anselm,
Acturally, the visualization is normal until the last snapshot of density step (the first one of equilibration). I do have several special residues in my system. However, I do not think it is a visualization problem. The reason is: when I perform the simulation on another machine (GPU version Amber18), all the results are normal; all the input files are same, and the only difference is the machine used to do the simulation. When I tried to use a CPU version (pmemd, amber16), the trajectory without restraints becomes abnormal.
Thanks anyway,
Zhanfeng
> -----原始邮件-----
> 发件人: "Dr. Anselm Horn via AMBER" <amber.ambermd.org>
> 发送时间: 2022-07-04 19:28:58 (星期一)
> 收件人: amber.ambermd.org
> 抄送:
> 主题: Re: [AMBER] atomic chaos in the equilibration trajectory
>
> 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_______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
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> >
>
>
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Received on Thu Aug 04 2022 - 13:34:11 PDT
