[gmx-users] atom types

[Mark Abraham]

On 02/08/11, Gavin Melaugh  <gmelaugh01 at 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 * <gmelaugh01 at 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 * <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?
> >>> ... 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 
> >>
> >
> 
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