[gmx-users] How to construct user specified bond potential

[Justin A. Lemkul]

Jia Haitao wrote:
> I have construct two table files: table_b0.xvg for A-A bond, 
> table_b1.xvg for B-B bond.
> and generated the bonds part of the topology file like this:
> [ bonds ]
> ; ai    aj     funct     table_number    k
>   1     2        8             0                1.000
>   2     3        8             0                1.000
> ...... 
>   55   56       8             1                1.000
>   56   57       8             2                1.000
> ......
> as force constant k is a function, so I set k = 1.000 and combine it with f.
>  
> Am I correct?

Probably not.  You've listed a table for n=2 but you don't actually use a 
table_b2.xvg, from what you've indicated.

Doing your own tests will be substantially faster than waiting for an email 
reply.  If you encounter a specific problem, post that.

-Justin

> Thank you very much. I really appreciate your help, Justin.
> 
> -- 
> */
> Jia Haitao
> State Key Laboratory of Polymer Physics and Chemistry
> Changchun Institute of Applied Chemistry
> Chinese Academy of Sciences
> Changchun 130022, CHINA
> /*

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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