[gmx-users] atom types

[Gavin Melaugh]

Hi Justin

Again thanks for the reply. I am not disagreeing with you but If I don't
include a [pairs] directive in the topology file (with gen_pairs =yes),
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?

Thanks

Gavin

Justin A. Lemkul wrote:
>
>
> 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
>>
>