I hope this doesn't come across as stupid, or worse insolent. But what is the point in stating the charges in the atom type section then ?
Gavin Mark Abraham wrote: > > > On 02/08/11, *Gavin Melaugh * <gmelaug...@qub.ac.uk> wrote: >> 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 ? > > The charges from [atoms] are used. The charges in [atomtypes] are > never used in any forcefield currently used with GROMACS. It might not > be possible for grompp to ever use them, but I'd have to check the > code for that. > > Mark > >> >> >> 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 -- 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