Hi,
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.
Thanks
Sanku
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