Ok. I understood. Thanks for your prompt reply.
On Fri, Dec 21, 2018 at 7:30 PM David A Case <david.case.rutgers.edu> wrote:
> On Fri, Dec 21, 2018, Rajarshi Roy wrote:
> >
> >I simulated a small glycan in an implicit solvent using igb=2. But
> >surprisingly the total energy and the potential energy of the system
> remain
> >positive. But the same structure in an explicit solvent is showing
> negative
> >total energy. Can anyone help me out from this? Is it normal to have
> >positive energy?
>
> The zero of energy is generally irrelevant in molecular mechanics
> calculations, and a positive potential energy is not necessarily a
> symptom of a problem.
>
> The explicit solvent calculation includes many favorable (negative)
> water-water interactions that are not present in the GB simulation. So
> the absolute energy is of little use: concentrate on energy differences.
>
> ....dac
>
>
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--
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Sat Dec 22 2018 - 02:30:02 PST
