[gmx-users] Potential Energy = -nan

[Justin A. Lemkul]

shikha agarwal wrote:
> 
> hi,
> I m tried nstxout=1 in my  .mdp file.
> 
> Potential Energy  =           -nan
> Maximum force     =  3.5637456e+07 on atom 2455
> Norm of force     =           -nan
> 
> 
> help me!
> 

The purpose of nstxout=1 is not to give you a different result.  It might aid 
you in watching the trajectory to determine what is going wrong.  From these 
values, and everything I have seen thus far, you have a physically unreasonable 
system.  Either you have atomic overlap or a topology problem.  Unless you 
provide substantially more diagnostic information, then pleas like "help me" 
will get you nowhere.  You haven't even provided a description of your system 
beyond "membrane protein."  The contents, topology sources, steps taken up until 
now, etc are all necessary pieces of information.

Please read the last sentence of the following page, and visit the link therein:

http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette

-Justin

> 
> regards:
> 
> shikha
> 

-- 
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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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