[gmx-users] Does shell molecular exclude core shell electrostatics automatically

[David van der Spoel]

Shuangxing Dai wrote:
> Hi, all,
> 
>             I was wondering if the shell molecular dynamics exclude the 
> electrostatic interaction automatically. According to the shell model, 
> the interaction between core and shell in replaced by the harmonic 
> interaction. If not, how to exclude electrostatic interaction between them?
> 
To know what happens you can check the list of exclusions in the tpr 
file using gmxdump. Then you can decide whether or not it is necessary 
to add an exclusion manually.


>             If I define in the top file:
> 
> [ defaults ]
> 
> ; nbfunc            comb-rule          gen-pairs           fudgeLJ fudgeQQ
> 
>   2                    1                      no                     
> 1.0        1.0
> 
>  
> 
> [ atomtypes ]
> 
> ;name  at.num      mass        charge   ptype       a          
> b                c
> 
>     O    8            15.99940       0.040       A   0.00000E-00   
> 0.00000E-00  0.00000E-00
> 
>    OS    8            0.00000      -2.040       S   0.00000E-00   
> 0.00000E-00  0.00000E-00
> 
>    ZN   30           65.37000       2.000       A   0.00000E-00   
> 0.00000E-00  0.00000E-00
> 
>  
> 
> [ nonbond_params ]
> 
>   ; i    j func           a             b            c
> 
>    OS         OS    2  9.21239E+05   4.56287E+01   3.08753E-03
> 
>    OS         ZN    2  5.11083E+04   2.79251E+01   0.00000E+00
> 
>    ZN         ZN    2  0.00000E+00   1.00000E+02   0.00000E+00
> 
>  
> 
> OS is shell and O is core for oxygen.
> 
>  
> 
>  
> 
> Thanks,
> 
> */Shuangxing Dai/*
> 
>  
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se