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

[Justin A. Lemkul]

Jia Haitao wrote:
> Manual section 4.2.13 maybe not enough. My potential functional shape is 
> much more complex. I need at least two different force constants as C6 
> and C12 in LJ potential function in section 6.7.2. 
> I use this for block copolymer system. There is only two types of 
> monomer(e.g. A, B) and two types of bond potential(e.g.A-A, B-B ). If I 
> can form two tables related to the two different bond potential 
> respectively (e.g. table 1 for A-A and table 2 for B-B), the problem 
> will be solved. Is it possible to be done in Gromacs?
> 

Yes.  This is not terribly clear in the manual, so I will update it, but you can 
indeed supply, i.e. table_b0.xvg, table_b1.xvg, table_b2.xvg, etc as necessary.

-Justin

> On Tue, Dec 7, 2010 at 11:14 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
>         /*
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> -- 
> */
> Jia Haitao
> State Key Laboratory of Polymer Physics and Chemistry
> Changchun Institute of Applied Chemistry
> Chinese Academy of Sciences
> Changchun 130022, CHINA
> /*

-- 
========================================

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

========================================