[gmx-developers] MPI crash with ghost molecules

[Anton Feenstra]

Jason de Joannis wrote:
> Naveen, I suppose the extra degrees of freedom affect the dynamics in a 
> small way. For example if you are using the Berendsen thermostat, the 
> velocity scaling factor depends upon the most recent kinetic temperature 
> which is proportional to the kinetic energy of the coupling group. 
> Therefore the ghost molecules will contribute to the scaling factor - 
> but anyways the temperature coupling should be preserved (and in my 
> simulations it is). It would probably be better to set the masses to 
> zero, but I was afraid of creating singularities in integration of the 
> bonded forces. i.e. dv/dt = f/m.

IIRC, atoms with zero mass are supported; they do not move at all.
But, this may not be what you want, either.

In addition, even without a direct influence like what you describe 
through the thermostat, additional degrees of freedom, even if 
uncoupled, will affect your thermodynamics (i.e., sampling/ensamble).


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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