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

[David van der Spoel]

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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