[gmx-users] Re: About Gromacs

[Mark Abraham]

Xi Ouyang wrote:
> Mark,
> 
>    Thank you for helping me in my questions.

Please keep GROMACS correspondence on the mailing list.

>    Right now I'm doing wavelet-based coarse-graining model of stretching 
> the protein. Wavelet is easy to play with under Matlab. Now I want to do 
> is try to do wavelet decomposition (like fourier decomposition) on the 
> potential function of the protein and try to do the MD, using the 
> decomposed potential. ( In Gromacs language, is potential contained in 
> the force field?? ) And comparing the computing time cost between the 
> original model and the decomposed model. But now I cannot find the 
> interface of the wavelet into gromacs.
>  
>    Because I am a EE guy, I know nothing about MD and gromacs. 
> Installing the gromacs under linux took me 2 weeks! So I really 
> appreciate your help if you can give me some advice. That will really 
> save me a lot of time.

First do some MDS background reading - such as the first few chapters of
the GROMACS manual. MDS are intrinsically atomistic, so you will need to
either cast your wavelet decomposition in such a fashion to use GROMACS,
or write custom software.

Mark