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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> > >
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>
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Received on Thu Aug 04 2022 - 13:34:03 PDT
