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. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? Many Thanks Gavin Mark Abraham wrote: > > > 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? > > Does manual section 5.3.4 answer your question? > > Mark > >> >> 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. 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