[gmx-users] Re: About Gromacs
Mark.Abraham at anu.edu.au
Tue Mar 24 06:32:39 CET 2009
Xi Ouyang wrote:
> 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.
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