On 02/08/11, Gavin Melaugh <gmelaug...@qub.ac.uk> wrote: > Hi Mark > > > Thanks for the reply. > I am currently reading that section of the manual and, unless I am > completely mistaken, it seems to vindicate what I am saying. > "Extra Lennard-Jones and electrostatic interactions between pairs of > atoms in a molecule can be added in the [pairs] section of a molecule > definition". > In my [atom types] directive I have atomtype, charge mass, sigma and > epsilon etc. All nonbonding parameters are then calculated according to > the combination rule (in my case 3). 1-4 interactions are then > calculated based on the information in [pairs] directive (all atoms are > three bond away). I just have the atom indices of each pair in this > directive therefore with gen_pairs = yes, the interaction parameters > between each pair (which are 1-4) are calculated based on Fudge LJ and > Fudge QQ (which are both 0.5 in my case). All of this in conjunction > with nrexcl =3. >
That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. > Or am I completely wrong? > In my set up then, are 1-4 Coulombic interactions determined by the pair > list and fudge QQ? > If the contradiction you think exists is this one... > > On 02/08/11, *Gavin Melaugh * <gmelaug...@qub.ac.uk> wrote: > >> Hi Justin > >> > >> Again thanks for the reply. I am not disagreeing with you but If I don't > >> include a [pairs] directive in the topology file (with gen_pairs =yes), > >> then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log > >> file. When I include the [pair s] directive then both types of > >> interaction are written to the log file. Therefore does gen_pairs= yes + > >> [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ > >> and QQ? > ... then 5.3.4 indicates that the presence of a [pairs] directive will generate the 1,4 output fields. The parameters for that output are taken from [pairtypes]. If gen-pairs=yes then the parameters are generated, else some warning/error occurs. The example in 5.7.1 has some more explanation about the use of the fudge parameters. Mark
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