[gmx-users] atom types
Mark Abraham
mark.abraham at anu.edu.au
Tue Aug 2 12:22:15 CEST 2011
On 02/08/11, Gavin Melaugh <gmelaugh01 at 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
> >>
> >
>
> --
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