Re: not a number error

From: Mohaddeseh Habibzadeh (
Date: Mon Jan 09 2017 - 08:07:12 CST

Thanks for your answer.
Do you mean the overlaps between the water in the box and the molecule? Is that because of large number of water molecules in the box?
How can I prevent exploding the system?
It may because of the bubble made in heating stage!
But the bubble disappears in frame 900 before it stopped by nan error!

On Mon, 01/09/2017 08:39 AM, Ajasja Ljubetič <> wrote:
> Just a guess (since you did not provide enough information): Probably your system is unstable and "exploded". This can happen if you're initial structure is not prepared correctly (i.e. has a large number of overlaps etc...)
> Check the last few lines in the NAMD log output.
> Best,
> Ajasja
> On 9 January 2017 at 08:53, Mohaddeseh Habibzadeh <> wrote:
> > ​​​Hello
> I was running npt MD with NAMD after minimization and heating
steps, and after passing 1700 frames normally, suddenly it wrote -nan in
 out put file for energies.
> And I couldn't see the pdb file after 1700 frame, it disapears!!
> May I know what's the reason and how it could be solved?
> Any help would be appreciated.

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