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?
Thanks Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Sorry to labour on this but: >> >> I don't quite understand what you mean when you say that nonbonded pair >> interactions are not Coulombic. Surely nonbonded charged atoms interact >> with each other, when close enough? (or by Nonbonded pair interactions >> do you explcitly mean 1-4,1-5, etc.) >> What are the 1-4 Coulombic interactions generated by, if not by >> gen_pairs =yes in my case? >> I have read this section of the manual loads and though I had a >> comprehensive understanding of it, but now I am confused again. >> > > Sure, there are nonbonded interactions for 1-4, 1-5, etc. But the > purpose of [pairtype] generation is for LJ terms only. They are > special 1-4 interactions between different atomtypes. Look at any > force field for which [pairtypes] are listed - they have only C6 and > C12 terms. Charges are not used for these calculations, but they are > applied later during the MD using normal Coulombic equations and FudgeQQ. > > -Justin > >> Thanks >> >> Gavin >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: >>>> Hi Justin >>>> >>>> I have checked the tpr file. Now it seems to assign the the two >>>> type of >>>> CHs as the same atom type, but at the same time with the specified >>>> charge from the [atoms] directive, as I expected. Concerning 1-4 >>>> interactions and gen_pairs =yes, my concern is this; from the pair >>>> list >>>> and using gen_pairs = yes, does grompp then take the 1-4 coulombic >>>> interaction for CH from the [atomtypes] directive (as the meaning of >>>> gen_pairs =yes)? >>>> Or does it assign the charge based on the atom index in the pair list? >>>> >>> 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. >>> >>> -Justin >>> >>>> Many Thanks >>>> >>>> Gavin >>>> >>>> Justin A. Lemkul wrote: >>>>> Gavin Melaugh wrote: >>>>>> Hi all >>>>>> >>>>>> A very quick question. I have an atom-type labelled CH in the >>>>>> atom-types >>>>>> with a particular charge, and in the atom list I assign some of >>>>>> these >>>>>> specific atoms with zero charge as below. When I generate 1,4 >>>>>> interactions using gen_pairs =yes, what charge for the CH type >>>>>> does it >>>>>> use? Does gromacs assign the CH with the different charge as a new >>>>>> atom >>>>>> type. >>>>>> >>>>> Charges set in [atomtypes] are not used. The zero charge is >>>>> assigned. Verify this by using gmxdump on your .tpr file. >>>>> >>>>> -Justin >>>>> >>>>>> ;Parameter level >>>>>> [defaults] >>>>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >>>>>> 1 3 yes 0.5 0.5 >>>>>> >>>>>> [atomtypes] >>>>>> ;type mass charge ptype sigma(nm) >>>>>> epsilon(kjmol-1) >>>>>> CB 12.011000 0.000000 A 0.355000 >>>>>> 0.292880 >>>>>> CA 12.011000 -0.115000 A 0.355000 >>>>>> 0.292880 >>>>>> HC 1.008000 0.115000 A 0.242000 >>>>>> 0.125520 >>>>>> CU 13.019000 0.265000 A 0.350000 >>>>>> 0.334720 >>>>>> NU 14.007000 -0.597000 A 0.325000 >>>>>> 0.711280 >>>>>> CH 13.019000 0.332000 A 0.385000 >>>>>> 0.334720 >>>>>> C3 15.035000 0.000000 A 0.391000 >>>>>> 0.669440 >>>>>> C2 14.027000 0.000000 A 0.390500 >>>>>> 0.493712 >>>>>> >>>>>> ;Molecular level >>>>>> [moleculetype] >>>>>> ; name nrexcl >>>>>> isotridecylcage 3 >>>>>> >>>>>> [atoms] >>>>>> ................. >>>>>> 72 CH 1 CGE CH 24 0.3320 13.0190 >>>>>> 73 C2 1 CGE C2 25 0.0000 >>>>>> 14.0270 >>>>>> 74 C2 1 CGE C2 25 0.0000 >>>>>> 14.0270 >>>>>> 75 C2 1 CGE C2 25 0.0000 >>>>>> 14.0270 >>>>>> 76 C2 1 CGE C2 26 0.0000 >>>>>> 14.0270 >>>>>> 77 C2 1 CGE C2 26 0.0000 >>>>>> 14.0270 >>>>>> 78 C2 1 CGE C2 26 0.0000 >>>>>> 14.0270 >>>>>> 79 C2 1 CGE C2 27 0.0000 >>>>>> 14.0270 >>>>>> 80 C2 1 CGE C2 27 0.0000 >>>>>> 14.0270 >>>>>> 81 C2 1 CGE C2 27 0.0000 >>>>>> 14.0270 >>>>>> 82 C2 1 CGE C2 28 0.0000 >>>>>> 14.0270 >>>>>> 83 CH 1 CGE CH 28 0.0000 >>>>>> 13.0190 >>>>>> 84 C3 1 CGE C3 29 0.0000 >>>>>> 15.0350 >>>>>> >>>>>> >>>>>> Many Thanks >>>>>> >>>>>> Gavin >> > -- 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
