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. 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
