[gmx-developers] MPI crash with ghost molecules

Jason de Joannis jdejoan at emory.edu
Tue Nov 7 00:16:08 CET 2006

>> 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.
I tried zeroing the masses and invmass. After about 3000 steps I 
started getting LINCS warnings. This happens even if I use 1e-30 
instead of zero for invmass.

\ Jason de Joannis  \
\ Emory University  \
  \ jdejoan at emory.edu \
   \ 404-402-1332      \

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