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? Thanks, Richard -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
