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 - 09:00:07 PST
