[gmx-users] regarding gen-pairs

[Gavin Melaugh]

Hi guys
> Sorry about the wrong subject in the previous e-mail. (I just hit reply).
> I have been running gromacs for a few months now with no real problems
> however some of my numbers differ from my supervisor's who uses DL-POLY.
> Anyway discussion of the discrpnacies has led me to questioning aspects
> of my topology file below (exerpts). We created the topology ourselves.
> I always thought that the set up below would calculate 1-4 interactions,
> but having read through the archives I am now confused. Do I have to
> give a pair list in topology file, or is gen-pairs = yes sufficient. I
> never created a pairlist as I thought that gen-pairs would create it
> from the parameters in atomtypes.
>
> ;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      0.390500      0.732200
>    C2     14.027000      0.000000       A      0.390500      0.493712
>
> ;Molecular level
> [moleculetype]
> ;       name         nrexcl
>        subhexylcage      3
>
> [atoms]
> ; atomnr  type   resnr  residue   name    cgnr     charge     mass
>     1      CA       1    CGE       CA       1     -0.1150     12.0110
>     2      CB       1    CGE       CB       1      0.0000     12.0110
>
> [bonds]
> ;  ai    aj   func   b0(nm)       kb(kjmol-1 nm-2)
>     1     2     1     0.1400      392459.2
>     1     6     1     0.1400      392459.2
>
> [angles]
> ;  ai    aj    ak   func  theta(deg)    ktheta(kjmol-1 rad-2)
>     2     1     6     1     120.00      711.2800
>     2     1     7     1     120.00      292.8800
>
> [dihedrals]
> ;  ai    aj    ak    al    func       V1           V2            
> V3            V4 (all kj mol-1)
>     1     2     3     4       5       0.00000      30.33400      
> 0.00000       0.00000
>     1     2     3    10       5       0.00000      30.33400      
> 0.00000       0.00000
>
> ;System level
> [system]
> ;the name of this system
> config test of 32 subhexyl cage molecules
>
> [molecules]
> ; moleculename     number
>  subhexylcage        32
>
>