[gmx-users] atom types

[Gavin Melaugh]

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?

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
>