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

[David van der Spoel]

james zhang wrote:
> 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?
how about the defaults section (chapter 5)
> 
> 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 
> <mailto: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/>
>      >
>     <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
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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> 
> 
> 
> -- 
> 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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