[gmx-users] Re: amber parameters in gromacs
alanwilter at gmail.com
Thu Jul 1 10:44:40 CEST 2010
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.
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.
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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