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'.
<snip>
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
--
========================================
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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