Hi Jason,
Thanks a lot for replying.
However, I have performed my simulation by EXACTLY following the before
said tutorial.
The tutorial is for amber 14 and I am using amber 11. But I don't think it
could be a problem.
So, what could be the way out?
Thanks again.
Sudip
On Wed, Jan 13, 2016 at 10:20 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Jan 13, 2016 at 10:19 AM, Sudip Das <das.sudip37.gmail.com> wrote:
>
> > Dear All,
> >
> > I am very new to AMBAR. I am performing a simulation of alanine dipeptide
> > in water following this tutorial:
> >
> > http://ambermd.org/tutorials/basic/tutorial0/
> >
> > Upto minimization step, it is running fine. But while heating, system is
> > showing bizarre bonds, angles and dihedrals.
> >
> > What could be the problem?
> >
>
> Could be visualization (did you use the PDB file to visualize in VMD?)
> Could be bad parameters, too high temperature, ... there are many ways to
> run a simulation incorrectly (and many ways a "correctly-run" simulation
> can behave poorly). Without knowing specific details of what you did
> (exact inputs and outputs, for instance), it's impossible to know where to
> even begin figuring out what (if anything) went wrong.
>
>
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Jan 13 2016 - 21:00:03 PST
