[gmx-users] atom types

[Justin A. Lemkul]

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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