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
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