On Apr 9, 2013, at 9:07 PM, moitrayee.mbu.iisc.ernet.in wrote:
> Dear Amber Users,
> I am trying to follow the protocols in
> http://ambermd.org/tutorials/basic/tutorial3 to obtain some conformational
> sampling for a small peptide of my interest. It turns out that during the
> heating stages (~250K), the total energy of the system becomes +ve. I am heating
> it upto 310K and I have pasted below the snapshots from the last heating run. I
> am following the protocol in the tutorial.
>
> NSTEP = 39950 TIME(PS) = 49.975 TEMP(K) = 310.94 PRESS = 0.0
> Etot = 221.9592 EKtot = 457.8622 EPtot = -235.9030
> BOND = 122.9774 ANGLE = 355.1161 DIHED = 464.4054
> 1-4 NB = 122.0431 1-4 EEL = 1446.9111 VDWAALS = -166.7690
> EELEC = -2024.7384 EGB = -555.8486 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
>
>
> KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
>
> Translational and rotational motion removed
>
> KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
>
> NSTEP = 40000 TIME(PS) = 50.000 TEMP(K) = 306.34 PRESS = 0.0
> Etot = 222.0932 EKtot = 451.0901 EPtot = -228.9969
> BOND = 116.2790 ANGLE = 351.3472 DIHED = 469.2875
> 1-4 NB = 118.3938 1-4 EEL = 1474.4917 VDWAALS = -165.3935
> EELEC = -2042.9887 EGB = -550.4139 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
> Any comments would be greatly appreciated.
A couple comments. I'm guessing this is an implicit solvent simulation, which tends to have much higher energies (since the water-water energies are very stabilizing). This is not unusual, especially for a small system.
Second, the potential energy is still negative, and that is what is usually used in conformational analyses.
Lastly, and far more importantly, absolute energies are completely meaningless. For example, a bond at its equilibrium value has an energy of 0 kcal/mol. If you run a qm calculation, it will be very negative. Only relative energies (differences between different structures are meaningful).
The short story, having positive energies may be an indication that something is wrong, but it certainly does not mean that something is definitely wrong.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 09 2013 - 20:00:03 PDT
