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

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed Oct 14 12:56:43 CEST 2015


This is a user question, not a developer question, so I reply too the user list.

Normally, they do not have bonded interactions between them. And unless they have identical sequence, they are two molecule types.

Kind regards,

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

> On 14 Oct 2015, at 10:49, toannt <toannt at vnu.edu.vn> 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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