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

[Mark Abraham]

Hi,

Please ask questions related to GROMACS use on the users mailing list. This
channel is for code development.

Mark

On Wed, Oct 14, 2015 at 2:05 PM toannt <toannt at vnu.edu.vn> wrote:

> Hi,
>
> Thanks. I'm defining two molecules types, each type have only one
> molecule in the simulation. When I said custom bonds, I was referring to
> the hydrogen bonds between the two strands. I'd like to understand how
> these bonds are handled by Gromacs in an atomistic simulation? If I have
> two strands at some distance apart, do they naturally come to each other
> to form the dsDNA?
>
> By the way, I am doing a grand canonical simulation, but I'd like to
> reuse libgromacs to avoid reinventing the wheel with some functions.
>
> Toan
>
> Vào ngày 14-10-2015 17:56, Berk Hess viết:
> > Hi,
> >
> > 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.
> >
> > Cheers,
> >
> > Berk
> >
> > 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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