[gmx-users] atom types
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 2 14:10:36 CEST 2011
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
> My sequence of 1-4 interaction generation should go like this I suppose:
> 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?
> Many Thanks
> 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
>>> 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
>>>>> include a [pairs] directive in the topology file (with gen_pairs
>>>>> 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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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