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
> >
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Received on Thu Aug 04 2022 - 13:34:02 PDT
