[gmx-users] atom types

[Justin A. Lemkul]

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
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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