[gmx-users] atom types

[Gavin Melaugh]

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 ?

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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