[gmx-users] atom types

Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Aug 2 14:24:18 CEST 2011

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 ?


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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