Hi Justin I see that we may have got our wires crossed from the off. Consider the [pairs] directive, which determines which atoms interact in a 1,4 manner. Consider two atoms listed the [pairs] directive. From the point of the Coulombic interaction between these two atoms I suppose my original question should have been: Does mdrun, when calculating the Coulombic potential between these two atoms, use the charges assigned to the atoms in the [atomtypes] directive or [atoms] directive ?
Cheers Gavin Justin A. Lemkul wrote: > > > 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." >> > > Charges *are* irrelevant - the information is not used when generating > pairs, which I thought was the original question. The charge > information is used during MD, when the pair list tells mdrun which > atoms interact in what way. Then you get Coul. 1-4 terms. Perhaps I > missed your point, but this whole thread started as "which charge is > used to generate pairs?" The answer is still none. > >> 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? >> > > Yes. > > -Justin > >> 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