[gmx-users] atom types

Mark Abraham mark.abraham at anu.edu.au
Tue Aug 2 14:54:42 CEST 2011 


On 02/08/11, Gavin Melaugh  <gmelaugh01 at qub.ac.uk> wrote:
> I hope this doesn't come across as stupid, or worse insolent. But what
> is the point in stating the charges in the atom type section then ?
> 

It would make sense for a force field that had a fixed charge for some/all atom types. If any such force fields exist, they don't get used for biomolecular MD. I don't know if such a force field can be implemented in GROMACS (per my earlier comment about checking the code). In some cases, grompp does a bunch of fancy footwork to try to infer the format of the content of the input lines. It's possible it can recognize that a charge field is missing and perhaps the charge gets read from [atomtypes] - but that is just not useful for biomolecular MD.

Another possibility is that the file formats serve other purposes (possibly in the distant past).

Mark


> 
> 
> Gavin
> 
> Mark Abraham wrote:
> >
> >
> > 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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