[gmx-users] Molecular dynamic simulations of Protein-DNA complex

[Mark Abraham]

Hi,

But the "global shape" and "structural flexibility" are different things.
Perhaps you shoudl make some screenshots, upload them to a file sharing
service and share the links with the list? (No attachments can be accepted
by the list.)

Mark

On Mon, Oct 24, 2016 at 11:19 AM Khadija Amine <kh.amine1 at gmail.com> wrote:

> Hello Erik,
>
> Thank you.
>
> I mean that the global shape of the complex is lost from 5ns to 10ns.
> After that, the structural flexibility of the complex is regained.
>
>
>
>
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Mon, Oct 24, 2016 at 11:06 AM, Khadija Amine <kh.amine1 at gmail.com>
> wrote:
>
> > Dear Gromacs users,
> >
> > I have run 20ns of MD simulations of my protein-DNA complex.
> >
> > All my trajectory files have been combined in a same final file.
> >
> > I have visualized that trajectory file using pymol software.
> > Unfortunately, the DNA structure and some parts of the complexed protein
> > structure show deformations.
> >
> > How can I prevent this issue and obtain correct structure, movement of my
> > complex?
> >
> > This is the first time I perform MD for the protein - DNA complex.
> >
> > Thank you
> >
> > *Khadija AMINE*
> >
> >
> > *Computational Biology*
> > *Postdoctoral Research Associate*
> > *Carnegie Mellon University*
> >
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