On Wed, Apr 20, 2016, yuandandan wrote:
> My system is one 1,2-dichloroethane molecules and 62 cyclohexane molecules.
>
>
> Please note that Etot = 1744.8560 and EELEC = 89.2662, they are both
> positive values, is there something wrong?
Probably not. If you have not yet done so, be sure to visualize your
simulation (after performing an autoimage transformation in cpptraj, to
collect all molecules back to a single unit cell.) That will give you a good
idea of what is happening, and will alert you to possible problems.
Also, check that the converged density of your system matches what you expect,
which is presumably close to the density of pure cyclohexane.
>
> I have checked the energy terms in the amber tutorial and found that
> both the EELEC values and Etot values are very negative.
Not sure what you are looking at, but systems in water have lots of attractive
hydrogen bond interactions, that lead to negative electrostatic energies. The
same might well not be true for cyclohexane.
....dac
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Received on Thu Apr 21 2016 - 05:30:04 PDT
