[gmx-users] a question about inner loop

[Fan Hao]

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 :-)

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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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