On Thu, Jan 14, 2016, Sudip Das wrote:
> 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?
Did you consider the previous suggestions from Jason?
> > >
> > > Upto minimization step, it is running fine. But while heating, system is
> > > showing bizarre bonds, angles and dihedrals.
*Exactly* how did you decide that the system was showing bizarre bonds, etc.?
And, it is not even clear what you mean here: are the bond energies bizarre?
Or is it the geometry of the molecule that is bizarre?
Did you examine the mdout file for the heating step? How does it compare with
the heating step mdout files provided in the tutorial? Same question for the
minimization step.
Note that the tutorial uses sander, which is now a part of AmberTools. So
there is really no reason here for you to be using Amber11 at all, at least as
far as I understand your situation.
...dac
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Received on Thu Jan 14 2016 - 05:00:05 PST
