Thanks, Jason! Maybe I didn't express it clearly.The work get shake erreos with a timestep of 1 fs. In order to see what's wrong, I have tried one production with a timestep of 0.5 fs and printed out the result every 1 step. But the similation ended up normally with a very large output file. And I couldn't open it. At that moment, I think there is nothing wrong with my system.
So I redo the preoduction with the result printing out every 1000 steps(timestep 0.5 fs), then there are many vlimit warnings. But the work continue. I wonder if the work succeeds, may I believe the result? And what can cause such vlimit warnings?
Thanks~
> -----原始邮件-----
> 发件人: Jason Swails <jason.swails.gmail.com>
> 发送时间: 2015年9月21日 星期一
> 收件人: AMBER Mailing List <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] SHAKE&Vlimit
>
> On Sun, Sep 20, 2015 at 9:56 PM, 罗艳玲 <201421150057.mail.bnu.edu.cn> wrote:
>
> > Dear all,
> > I want to preform a MD calculation of my protein, but there are problems
> > that have bothered me for a long time. After I minimized, heated and
> > equilibrated the system before the MD, there is no problem. Then the MD
> > calculation always stopped with a SHAKE error and many vlimit reminds. I
> > have searched on the Internet and mailing list, and tried heating slowly
> > and did the MD with a smaller timestep(0.5 fs), the problem still exist
> > with many vlimit reminders. What can I do now? Look forward to your reply.
> > The input and output files are shown here:
> >
>
> In the simulation where you get vlimit warnings and eventual SHAKE errors,
> you should print out energies to the mdout file and coordinates to the
> trajectory very frequently so you can try to capture what may be happening
> in a visualization program.
>
> There are too many things that could be going wrong that are *unrelated* to
> the mdin file that it's impossible to determine simply from the information
> you gave.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 21 2015 - 05:00:03 PDT
