[gmx-users] pdb2gmx pairs clarification

Richard Broadbent richard.broadbent09 at imperial.ac.uk
Wed Jan 11 20:11:27 CET 2012

Dear All,

I've been reading the manual (v4.5.4) and could use a small amount of
clarification. On p117 it says:

pdb2gmx sets the number of exclusions to 3, which means that
interactions between atoms connected by at most 3 bonds are excluded.
Pair interactions are generated for all pairs of atoms that are
separated by 3 bonds (except pairs of hydrogens)...

Does the last part mean that hydrogen atoms separated by precisely 3
bonds are not subject to fudge factors in MD simulations?



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