On Tue, Jan 25, 2005, Venkata S Koppuravuri wrote:
>
> First i tried in the presence of water and everything went fine. But when
> I try to do the same without water the simulation gives the following
> output
>
> --------------------------------
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 nan nan 1.2155E+02 O 2351
>
> BOND = 1307.4974 ANGLE = 3088.3520 DIHED = 4822.5876
> VDWAALS = 1321392.7282 EEL = -76345.8040 EGB = nan
> 1-4 VDW = 3348.7754 1-4 EEL = 42319.0282 RESTRAINT = 0.0000
> -----------------------------------
Your vdw energy is very high, so you still have a bad structure, but that
doesn't explain that NaN for EGB.
Try an intial minimization with igb=0, ntb=0 (no water), and then turn on
GB. But you will probably have to post your input files, since otherwise
I can't see what is going on.
> nsnb = 25, cut = 8.0,
Unrelated to the above: you should use a cutoff much bigger than 8.0 for
GB calculations (try 15-20 Ang.).
....good luck...dac
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Received on Tue Jan 25 2005 - 22:52:59 PST
