(meant to sent this to the whole amber list; augments what Jason said)
> NSTEP = 177900 TIME(PS) = 357.800 TEMP(K) = 329.83 PRESS = -40.7
> Etot = 3895.3213 EKtot = 2619.1565 EPtot = 1276.1648
> BOND = 570.2390 ANGLE = 1053.1037 DIHED = 688.1559
> 1-4 NB = 961.6047 1-4 EEL = -963.6260 VDWAALS = -1601.8145
> EELEC = 568.5021 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 199.0413 VIRIAL = 234.9427 VOLUME = 40887.3038
>
> Why is EPtot positive?
> Why are the Angle, Bond, and DIHED so huge ?
Why not? What happens if you add thermal fluctuations (~kT) per degree of
freedom to each degree of freedom. What should happen to a bond or angle?
What is the zero of energy? (perhaps no deviation from the ideal bond or
angle length/angle).
Can you have a negative bond energy? (No) Will bonds deviate with
thermal fluctuation? Yes. Will this be a positive energy? I hope so.
What about vdw's? If they are all positive, we are in trouble. Why?
Atomic overlap. With the 6-12, at short range very unfavorable, at short
to mid, favorable (negative), at long range still not exactly zero
(meaning still favorable). If you have positive vdw means clash.
> What is wrong with the set up?
Nothing, likely, but I cannot decipher further without seeing the data.
--tec3
p.s. we can (and do) in our molecular mechanics potential arbitrarily
define our zero's. We could make dihedrals negative, positive, whatever.
Key is the *relative* energies. With MM we cannot compare energies of
different molecules easily (since we haven't calibrated the zeros) and you
need to think about the potential and what these energies mean or represent.
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Received on Mon Feb 29 2016 - 21:00:03 PST
