On 02/08/11, Gavin Melaugh <gmelaug...@qub.ac.uk> wrote: > 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 ? >
It would make sense for a force field that had a fixed charge for some/all atom types. If any such force fields exist, they don't get used for biomolecular MD. I don't know if such a force field can be implemented in GROMACS (per my earlier comment about checking the code). In some cases, grompp does a bunch of fancy footwork to try to infer the format of the content of the input lines. It's possible it can recognize that a charge field is missing and perhaps the charge gets read from [atomtypes] - but that is just not useful for biomolecular MD. Another possibility is that the file formats serve other purposes (possibly in the distant past). Mark > > > 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 > >
-- 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