Rolf Erwin Isele-Holder wrote:
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.
Have you tried actually using the Amber ports for Gromacs? You've got some
weird hybrid monster going on here, defining Gromos96 as your force field, then
trying to make it look like Amber. Lots of potential sources of error here.
I would strongly suggest having a look here:
http://ffamber.cnsm.csulb.edu/
-Justin
Regards,
Rolf
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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