AMBER Archive (2005)

Subject: Re: AMBER: NAN errors

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 25 2005 - 16:09:11 CST


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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu