Re: not a number error

From: Ajasja Ljubetič (
Date: Mon Jan 09 2017 - 07:39:15 CST

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
Check the last few lines in the NAMD log output.


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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