[gmx-users] amber parameters in gromacs

[Rolf Erwin Isele-Holder]

Dear gromacs-users,

I've been simulating a box of liquid glycerol. The parameter's I have used were taken from an article, whose authors achieved good agreement between their simulation and experiments. These authors used an amber force field and the software ORAC.

I used exactly the same parameters as them for my topology and very similar settings in my mdp file. However I did not get the same results as them. Do you know why I get these different results? I am in doubt weather the top of my topology is correct, so I pasted it here:

     #define _FF_GROMOS96
     #define _FF_GROMOS53A6

     [ defaults ]
     ; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
       1		2		yes		0.5	0.8333

     [ atomtypes ]
     ;name  at.num   mass      charge  ptype   sigma  epsilon
        OA     8     0.000      0.000   A      0.3442    0.879228
        C      6     0.000      0.000   A      0.3816    0.45803592
        H      1     0.000      0.000   A      0         0
        HC     1     0.000      0.000   A      0.2774    0.06573276


     [ moleculetype ]

     Glycerol      3
 
     [ atoms ]
     ;   nr      type  resnr resid  atom  cgnr   charge
         1         OA     1   GLCR   OAA    1      -0.585    15.9994
         2         H      1   GLCR   HAA    1       0.396    1.008
         3         C      1   GLCR   CAD    1       0.182    12.011
        .....

I think, that by specifying comb-rule = 2 giving sigma and epsilon is correct instead of c6 and c12. The 0.5 for fudgeLJ and the 0.8333 for fudgeQQ are supposed to lower the 1-4 interaction.

Regards,

Rolf