[gmx-users] Disable non-bonded interactions between molecules

ruehle at mpip-mainz.mpg.de ruehle at mpip-mainz.mpg.de
Mon Mar 7 22:32:33 CET 2011

Dear all,

I need to perform a simulation in which interactions between molecules  
(polymers) are calculated only via virtual sites. Within a molecule,  
non-bonded interactions between atoms should be present. Further, it  
would be best to be able to select which parts of the molecule  
explicitly interact (only close units along the chain).

What is the most efficient way to achieve this? Energy group  
exclusions are not possible since they would also disable  
intramolecular interactions. One possibility might be to set all  
non-bonded parameters (charge + lj) to zero and then explicitly  
specify the intramolecular ones as pairs:

I need coulomb (cut-off) as well as Lennard-Jones interactions
-> use pairs function type 2, just copy the charges + lennard jones parameters
What about 1-4 scaling? Can i just scale down charges + lennard jones  
parameters for those pairs or do I have to use fudge QQ in pairs?

Would this work or is there a better solution (maybe also with minor  
code changes)?

Thanks in advance for any hints,

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