[gmx-users] Re: amber parameters in gromacs

[Alan]

Hold on, you said *amber*, nevertheless you top has definitions for
GROMOS**. Either you are mixing force fields here (which *bad*) or worse,
your not using Amber FF, which is *really bad*.

I would be helpful if you give the commands you're using for pdb2gmx and
grompp. Besides, are you aware of ffamber and acpype? Since you said you
have the parameters for glycerol you may not need to build the topology
anew, but I do recommend looking at acpype.googlecode.com to know more about
simulations involving amber ff and gromacs, besides links to important
resources like ffamber.

Cheers,

Alan


On Thu, Jul 1, 2010 at 09:13, <gmx-users-request at gromacs.org> 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.
>
> Regards,
>
> Rolf
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100701/d6b420ba/attachment.html>