On Sat, Jul 24, 2010, Philippe Pinard wrote:
> In the meantime, I run an implicit solvent minimisation for 500 steps, and
> followed by an MD for 100 ps for equilibration at T=300K. The surprise, is that
> my potential energy is huge (bond and angle terms are soo big)!!
> NATOM = 2244 NTYPES = 8 NBONH = 1248 MBONA = 995
>
>
> NSTEP = 7400 TIME(PS) = 7.400 TEMP(K) = 291.54 PRESS = 0.0
> Etot = 4154.4925 EKtot = 1950.0576 EPtot = 2204.4348
> BOND = 812.4619 ANGLE = 1818.8081 DIHED = 446.1581
> 1-4 NB = 490.4294 1-4 EEL = -215.7047 VDWAALS = -972.2307
> EELEC = -11.1912 EGB = -164.2959 RESTRAINT = 0.0000
This is close to what you should expect: you have about 2250 bonds in
your system. In classical statistical mechanics, each bond would get kT/2 =
0.3 kcal/mol of average potential energy. You number is a bit higher than
that, but not by a lot. You have about twice as many angles as bonds, and
again equipartition would predict numbers not too different from what you
report. So, I think you conclusion that "bond and angle terms are soo big"
is not justified.
As suggested earlier, visualize you trajectory if you suspect problems (even
if you don't!)
....dac
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Received on Sat Jul 24 2010 - 21:00:03 PDT
