Hi Justin and Mark Fudge LJ is only used when gen_pairs =yes. Fudge QQ is used regardless. I suppose a more concise and sensible question is the following: Are the atoms involved in the 1,4 Coulombic interactions specified in the [pairs] directive? If not how else are they generated.
Cheers Gavin Gavin Melaugh wrote: > Yes I think the example vindicates what I am saying as well. I suppose I > the "contradiction" ( I'll call it the point of confusion) you refer to > is perhaps when Justin (who is always more than helpful) said that > "Charges are irrelevant for generation of pair interactions. Nonbonded > pair interactions are LJ, not Coulombic. You will certainly have 1-4 > Coulombic interactions, but they are not generated by gen_pairs. See > manual section 5.3.4." > > My sequence of 1-4 interaction generation should go like this I suppose: > > e.g. > [pairs] > 3 6 > no parameters present therefore get from [pairtypes] directive. > no [pairtypes] directive therefore get from [non_bonded parameters] > directive as gen pairs = yes > again no [non_bonded parameters] directive. > Therefore generate 1,4 interaction parameters based on the normal sigma > and epsilon values (comb rule 3) present in [atomtypes] directive, in > accordance with fudge LJ and QQ. > > My point is, then in conclusion, that in this way surely the 1,4 > electrostatic interactions are determined by the pair list and in my > case gen_pairs = yes.... no? > > Many Thanks > > Gavin > > > Mark Abraham wrote: > >> 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 >> > > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
