[gmx-users] reg error in coordinate file

Justin A. Lemkul jalemkul at vt.edu
Sun May 1 15:06:04 CEST 2011

vidhya sankar wrote:
> Dear gmx-user,
>                        when i run Equilibration Phase (nvt.mdp) i got 
> the .gro files as follows
> that is co-ordinates not defined in my .gro file
>  What should i change in my mdp file in order to remove 'nan' and to 
> obtain coordinate?

I doubt the problem is that simple.  "Nan" means "not a number," and thus 
represents some infinite value.  So either:

1. your system blew up at the last step when the .gro file was written
2. there is some bug that needs to be fixed
3. your file system had some problem writing the .gro file

To address (1), check the .log file for any pertinent messages about 
instability.  For (2), you'll have to at least provide your Gromacs version, 
input settings (.mdp file), and perhaps a description of the hardware.  For (3), 
check your output trajectory with gmxcheck and/or watch it in VMD (or your 
favorite viewer) and if its contents are normal and the .gro file is the only 
aberrant output, then it's your file system's fault, no Gromacs'.


>    6.56000   4.36200  12.00000

For a system of just 80 atoms, this box seems extraordinarily large.  Quite 
likely your system blew up.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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