[gmx-users] Potential Energy = -nan

[Justin A. Lemkul]

shikha agarwal wrote:
> hi
>  >  I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk .

What is the hardware type?  PowerPC, Intel 32- or 64-bit, etc?

> when i skiped scaling by factor 0.95 then , after EM step I m getting 
> same potential energy nan result.
> 

Do other simple systems work?  Can you do simple tutorial systems like lysozyme 
in water?

Otherwise, you've got some topology problem that prevents the system from being 
properly minimized.  Set nstxout=1 in your .mdp file and watch what's happening.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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