[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion

[james zhang]

I did convert the parameters according to Manual chapter 4.11 and 5.3.3.
I used C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula.
If my conversion is right, then where is wrong?

I find the same question in the mailing list, but there is no response.
http://www.gromacs.org/pipermail/gmx-users/2004-July/011337.html

Why did the same system get totally different simulation result when I
changed the L-J expressions?
Thanks.

On 7/15/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> james zhang wrote:
> > Hi,
> >
> > I am trying to do some simulation of chloroform system and I need
> > convert sigma & epsilon to C6 & C12 LJ-parameters.
> >
> > I use C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula.
> > This is my result
> >
> > [ atomtypes ]
> > ;type    mass    charge       ptype          sigma      epsilon
> >  CH      12.01100   0.420       A        3.80000e-01  3.26944e-01
> >  CLCL3   35.45300  -0.140       A        3.47000e-01  1.25604e+00
> >
> > [ atomtypes ]
> > ;name  at.num      mass        charge   ptype       c6           c12
> >    CH    6      13.01100       0.000       A   0.39376E-02   0.11856E-06
> >   CL3   17      35.45300       0.000       A   0.87710E-02
> 0.15300E-06
> >
> >
> > The sigma and epsilon LJ-parameters is very good to discribe chloroform
> > box in the molecular topology of user contributions.
> >
> http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/
> > <
> http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/
> >
> > But when I use C6&C12 LJ-parameters I can not get equilibrium and the
> > moleculars sticked together.
> >
> cd src/contrib/
> make sigeps
> manual chap. 4
> check combination rules
>
> > Thanks in advance.
> >
> > --
> > Sincerely yours,
> > James Jianzhang
> >
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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-- 
Sincerely yours,
James Jianzhang
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