[gmx-users] a question about inner loop

[Erik Lindahl]

Hi Hao,

Yes, that's the loops you are using, although there might be  
coulomb-only and/or LJ-only loops to.

Cheers,

Erik

On Tuesday, Mar 11, 2003, at 06:51 US/Pacific, Fan Hao wrote:

>
> Hi, people:
>         I am not sure with some codes in the innerc.c of gromacs3.0.5,
> so I raise them here to see whether my understanding is correct.
> In my simulation, I use Reaction-Field and cut-off for coulomb and lj,
> with spc water as my solvent. Do they correspond to the following  
> process?
>         1) inl2100  for interactions of protein.
>                       Forces:      Calculated
>                       Coulomb:     Reaction field
>                       Nonbonded:   Lennard-Jones
>                       Solvent opt: No
>                       Free energy: No
>       + 2) inl2120  for interactions between protein and water
>                       Forces:      Calculated
>                       Coulomb:     Reaction field
>                       Nonbonded:   Lennard-Jones
>                       Solvent opt: Water (3 atoms) - other atom
>                       Free energy: No
>       + 3) inl2130  for interactions between water and water
>                       Forces:      Calculated
>                       Coulomb:     Reaction field
>                       Nonbonded:   Lennard-Jones
>                       Solvent opt: Water (3 atoms) - water (3 atoms)
>                       Free energy: No
> my mdp file is like:
>         coulombtype              = Reaction-Field
>         rcoulomb                 = 1.4
>         epsilon_r                = 78
>         vdwtype                  = Cut-off
>         rvdw                     = 1.4
>
> Any help are sincerely appreciated!
>
> Best regards
>
> Yours sincerely
>
> Hao Fan :-)
>
> ----------------------------------------------------------------------- 
> --
> Drs. Hao Fan                            email F.Hao at chem.rug.nl
> Lab. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4                            9747 AG GRONINGEN
> The Netherlands
> ----------------------------------------------------------------------- 
> --
>
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