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

[Justin A. Lemkul]

Jia Haitao wrote:
> Hello, everyone
> 
> In gromacs user manual 6.7, they form non-bond potentials using table 
> files, What should I do if I want to use a new *Bond* potential? 
> The new bond potential combines two harmonic bond 
> potentials,  Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part is a 
> standard harmonic potential.
> Besides, according  user manual 5.7, there is 10 function types in table 
> 5.5. How can I use the 8th and 9th type?  Is there some examples? .    

All the information related to what you want to do is in the manual, section 
4.2.13.  Per the caption of Table 5.5, bond type 8 will be used to generate 
exclusions (when running grompp); presumably type 9 will not.  Hopefully someone 
will correct me if I'm wrong here.

-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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