[gmx-users] mdrun running without simulating new steps

[Justin A. Lemkul]

st wrote:
> Hi,
>  
> I run a two-molecule system with mdrun_d in a water box (~10000 water 
> molecules.)
> The program looks running properly (no errors nor warnnings)
> However the program seems stop outputting files (because the output file 
> size stop increases) after about 5min.
> The mdrun_d interface looks normal without any errors, the md.log 
> contains only two saves:

<snip>

> Grid: 9 x 9 x 14 cells
>    Energies (kJ/mol)
>            Bond          Morse          Angle       G96Angle    Proper Dih.
>     3.35232e+05    3.27635e+01    7.09937e+02    1.73811e+01    2.47097e+03
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>     1.48669e+05   -4.50390e+05   -1.89304e+04    1.78117e+04    4.38796e+05
>    Total Energy  Conserved En.    Temperature Pressure (bar)
>     4.56608e+05    4.56608e+05    1.09892e+03   -5.74950e+04
>  
>            Step           Time         Lambda
>             100        0.05000        0.00000
>  
>    Energies (kJ/mol)
>            Bond          Morse          Angle       G96Angle    Proper Dih.
>     3.38536e+05    1.06967e+03    2.21584e+04    4.26526e+01    3.13457e+03
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>     8.73487e+04   -5.64854e+05   -4.48577e+04   -1.57422e+05    3.56524e+05
>    Total Energy  Conserved En.    Temperature Pressure (bar)
>     1.99102e+05    7.60608e+05    8.92881e+02    7.56563e+04
>  

I'd say the system is exploding.  Your temperature is oscillating between 1000 K 
and 893 K using a Nose-Hoover thermostat, and your potential starts off in 
excess of 10^4 kJ mol^-1.  Did you run any sort of energy minimization or 
weak-coupling equilibration before this run?

It's odd that mdrun wouldn't give some sort of LINCS warning or write out 
step*.pdb files right beforehand, though.

-Justin

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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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