[gmx-users] atom types

[Justin A. Lemkul]

Gavin Melaugh wrote:
> 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.
> 

Sure, there are nonbonded interactions for 1-4, 1-5, etc.  But the purpose of 
[pairtype] generation is for LJ terms only.  They are special 1-4 interactions 
between different atomtypes.  Look at any force field for which [pairtypes] are 
listed - they have only C6 and C12 terms.  Charges are not used for these 
calculations, but they are applied later during the MD using normal Coulombic 
equations and FudgeQQ.

-Justin

> 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
> 

-- 
========================================

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

========================================