<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi,</div><div> 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)</div><div><br></div><div> If we choose charmm forcefield ( or opls forcefield) in pdb2gmx, it writes down the topology file topol.top </div><div> 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.</div><div> </div><div>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) . </div><div><br></div><div>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. </div><div>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 ?</div><div><br></div><div>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.</div><div><br></div><div>Thanks</div><div>Sanku</div></div></body></html>