[gmx-users] amber parameters in gromacs

[Justin A. Lemkul]

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

-- 
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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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