[gmx-developers] DNA is one moltype or two moltype?

Berk Hess hess at kth.se
Wed Oct 14 12:56:31 CEST 2015


There is no direct link between "real" molecules and molecule types. The 
only restriction is that you can only define chemical bonds between 
atoms within the same molecule type. Thus you can have two DNA strands 
in one or in two separate molecule types.
I don't understand what custom-bonds you are referring to. Usually DNA 
strands are not chemically bonded to each other.



On 10/14/2015 11:49 AM, toannt wrote:
> Hi all
> I've just started to look at libgromacs for a custom simulation. I'm 
> studying the gmx data structures to initialize them directly. I wonder 
> if molecules such as DNA is considered by gromacs to be two molecule 
> types (one for each strand) or is only one molecule type with some 
> custom-bonds between the two strands?
> Thanks
> Toan

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