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

[Jia Haitao]

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?

On Tue, Dec 7, 2010 at 11:14 PM, Justin A. Lemkul <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 | (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
*
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