[gmx-users] query on 1-4 interaction

Sanku M msanku65 at yahoo.com
Fri Jan 13 18:51:51 CET 2012

   I have a question regarding how the 1-4 interaction works in GROMACS4.5.4 with charmm force field and its relation with number of exclusions ( nrexcl)

 If we choose charmm forcefield ( or opls forcefield) in pdb2gmx, it writes down the topology file topol.top 
  with nrexcl 3 . If I try to understand what nrexcl = 3 means, I guess, it means that any non-bonding interactions among atoms which are upto 3 bonds away from each other are excluded.
However, at the same time, it also writes  down an extra block called '[Pair]' which I presume is 1-4 interaction where it enumerates all atoms which are within 4 atoms  ( such as 1 4, 2 5 etc in a linear chain) . 

I wonder, whether even with nrexcl = 3 ( suggesting exclusion of all nonbonding interactions within 3 bonds ) , whether this 1-4 interaction is actually added up in the energy calculations or in this case ( i.e with nrexcl=3)  the 1-4 interaction presented by [Pair] part is actually ignored. 
Or, should one change nrexcl to a value of 2 if one really needs to take into account the 1-4 interaction included in the [pair] part ?

Also,is there any difference between the functional form of 1-4 interaction and normal nonbonding interaction ? I presume both of them are treated as LJ interaction.

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