[gmx-users] initial temperature ridiculously high

[Justin A. Lemkul]

GZ Zhang wrote:
> Hi, ALL
> 
> I met a bizarre in a NVT simulation in which the initial temperature is 
> ridiculously high.
> Even though I specify the initial temperature to be 200 K.
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel                  = yes
> gen_temp                 = 200.0
> gen_seed                 = 173529
> 
> Energies (kJ/mol)
>            Bond           LJ (SR)                Coulomb (SR)    Coul. 
> recip.        Potential
>     7.17894e+01    3.25101e+05     -3.75274e+05   - 3.13877e+05   
> -3.63978e+05
>          Kinetic En.    Total Energy        Temperature      Pressure (bar)
>     7.97000e+04   -2.84278e+05     1.00007e+04      2.75198e+06
> 
> The force field I used is called 
> CLAYFF(http://www.sklogwiki.org/SklogWiki/index.php/CLAYFF_force_field), 
> in which all atoms except hydroxyl groups interact through non-bonded 
> vdW and electrostatic interactions.
>   
> What's more strange is that after 5 ps, the system converted from a 
> ordered layer structure 
> into a disordered structure, like melting, although temperature goes to 
> 200 K.
> 
> Any comments?
> 

The combination of high temperature and really high pressure (beyond the normal 
+/- 1000 fluctuations) suggests that you have an unreasonable starting structure 
  and/or broken topology.  Atomic overlap (or bad parameters) will cause atoms 
to shoot wildly across the system, leading to large velocities and high 
temperature.  In this case, you were fortunate that the whole system didn't 
explode but somehow continued.

-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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