Hi Jason,
This is with pmemd.cuda. I printed out each step just before the error
message happens and I found that the temperature rises very rapidly and the
box size decreases. I feel like this error might stem from the
equilibration of the system. I found that the error message did not arise
when I equilibrated my system for a longer amount of time.
Thanks,
Jordan
On Fri, Mar 6, 2015 at 2:22 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Mar 6, 2015 at 2:11 PM, Jordan Graziadei <jgraziad.hamilton.edu>
> wrote:
>
> > Hello again,
> >
> > I was wondering if anyone had any insight into the problem I'm having.
> I'm
> > trying to troubleshoot but am not making much progress.
>
>
> I'm a bit puzzled about why you're getting that error as well. I wonder
> if there is some sort of catastrophic box collapse that is happening,
> although I don't know what could or would cause that.
>
> Is this with sander? pmemd? pmemd.cuda? Does the same thing happen with
> any of the *other* programs? Have you tried printing every step close to
> when that error occurs?
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Mar 12 2015 - 10:00:02 PDT
