[gmx-users] Re: periodic molecule

Valentina valentina.erastova at durham.ac.uk
Wed Sep 18 16:10:39 CEST 2013

On restraining bonds:

The atom moves across the basic unit, i.e. it is not recognising that it
should bond via periodic_molecule

Error: The charge group starting at atom 2833 moved than the distance
allowed by the domain decomposition (1.615483) in direction X

In any case (restraining or not all-bonds) when I am doing grompp, I get a
warning - 
WARNING 1 [file LDH21/em.mdp]:
  The sum of the two largest charge group radii (1.062153) is larger than
  rlist (1.000000)

I decided to take it as a healthy one, as according to

this is because of 
"Molecules are broken across periodic boundaries, which is not a problem in
a periodic system.  In this case, the sum of the two largest charge groups
will correspond to a value of twice the box vector along which the molecule
is broken."

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