[gmx-users] constraining two diff molecules removes LJ interaction?

Guilherme Menegon Arantes garantes at iq.usp.br
Fri Oct 26 15:35:24 CEST 2007

This is my first post to this list, so a warm hello to everybody!

I want to constrain the distance between two atoms in different
molecules (two diff proteins, in complex). So, I defined both molecules
in the same [ moleculetype ] and added an extra [ bonds ] line: 
216   6465     6 0.400 300.00 ; 
(notice it is type 6, for harmonic constrain). The constrain seems to 
work fine, but it looks that LJ interaction between the centers is also 
removed (or scaled) since grompp gives me LJ14:   31800 with the 
constrain and  LJ14:   31799 without it (I am guessing that this LJ14 is 
the number of 1-4 exclusions from the LJ pair list , correct?). But 
since these two centres (216 and 6465) are actually in different 
molecules, their LJ interaction should be included.

The manual says ``There is a harmonic interaction ([ bonds ] type 6) 
which does not connect the atoms by a chemical bond''. So, why do I see
an increase in the LJ14 number? Should I re-include this LJ interaction
using [ pairs ]? Which type? Need to re-assing the C6 and C12 coeff.?

Thanks for your help,



Guilherme Menegon Arantes, PhD       São Paulo, Brasil

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