[gmx-users] atom types

[Gavin Melaugh]

Hi Justin

Sorry to labour on this but:

I don't quite understand what you mean when you say that nonbonded pair
interactions are not Coulombic. Surely nonbonded charged atoms interact
with each other, when close enough? (or by Nonbonded pair interactions
do you explcitly mean 1-4,1-5, etc.)
What are the 1-4 Coulombic interactions generated by, if not by
gen_pairs =yes in my case?
I have read this section of the manual loads and though I had a
comprehensive understanding of it, but now I am confused again.

Thanks

Gavin
Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> I have checked the tpr file. Now it seems to assign the the two type of
>> CHs as the same atom type, but at the same time with the specified
>> charge from the [atoms] directive, as I expected. Concerning 1-4
>> interactions and gen_pairs =yes, my concern is this; from the pair list
>> and using gen_pairs = yes, does grompp then take the 1-4 coulombic
>> interaction for CH from the [atomtypes] directive (as the meaning of
>> gen_pairs =yes)?
>> Or does it assign the charge based on the atom index in the pair list?
>>
>
> 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.
>
> -Justin
>
>> Many Thanks
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
>>>> Hi all
>>>>
>>>> A very quick question. I have an atom-type labelled CH in the
>>>> atom-types
>>>> with a particular charge, and in the atom list I assign some of these
>>>> specific atoms with zero charge as below. When I generate 1,4
>>>> interactions using gen_pairs =yes, what charge for the CH type does it
>>>> use? Does gromacs assign the CH with the different charge as a new
>>>> atom
>>>> type.
>>>>
>>> Charges set in [atomtypes] are not used.  The zero charge is
>>> assigned.  Verify this by using gmxdump on your .tpr file.
>>>
>>> -Justin
>>>
>>>> ;Parameter level
>>>> [defaults]
>>>> ; nbfunc    comb-rule     gen-pairs        fudgeLJ     fudgeQQ
>>>>      1         3              yes            0.5         0.5
>>>>
>>>> [atomtypes]
>>>> ;type     mass           charge      ptype     sigma(nm)  
>>>> epsilon(kjmol-1)
>>>>    CB     12.011000      0.000000       A      0.355000      0.292880
>>>>    CA     12.011000     -0.115000       A      0.355000      0.292880
>>>>    HC      1.008000      0.115000       A      0.242000      0.125520
>>>>    CU     13.019000      0.265000       A      0.350000      0.334720
>>>>    NU     14.007000     -0.597000       A      0.325000      0.711280
>>>>    CH     13.019000      0.332000       A      0.385000      0.334720
>>>>    C3     15.035000      0.000000       A      0.391000      0.669440
>>>>    C2     14.027000      0.000000       A      0.390500      0.493712
>>>>
>>>> ;Molecular level
>>>> [moleculetype]
>>>> ;       name         nrexcl
>>>>         isotridecylcage      3
>>>>
>>>> [atoms]
>>>> .................
>>>>  72      CH       1   CGE        CH      24      0.3320     13.0190
>>>>    73      C2       1   CGE        C2      25      0.0000     14.0270
>>>>    74      C2       1   CGE        C2      25      0.0000     14.0270
>>>>    75      C2       1   CGE        C2      25      0.0000     14.0270
>>>>    76      C2       1   CGE        C2      26      0.0000     14.0270
>>>>    77      C2       1   CGE        C2      26      0.0000     14.0270
>>>>    78      C2       1   CGE        C2      26      0.0000     14.0270
>>>>    79      C2       1   CGE        C2      27      0.0000     14.0270
>>>>    80      C2       1   CGE        C2      27      0.0000     14.0270
>>>>    81      C2       1   CGE        C2      27      0.0000     14.0270
>>>>    82      C2       1   CGE        C2      28      0.0000     14.0270
>>>>    83      CH       1   CGE        CH      28      0.0000     13.0190
>>>>    84      C3       1   CGE        C3      29      0.0000     15.0350
>>>>
>>>>
>>>> Many Thanks
>>>>
>>>> Gavin
>>
>