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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 21 2015 - 04:30:06 PDT
