[gmx-users] analyzing docking + MD results

[MD]

Hi Mark,

Does GROMACS do that or I need to go with other software?

Thank you,

Ming

On Dec 23, 2017 6:06 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Normally one would try to compute the relative free energy of binding
> between the two poses, but that is rather more costly than what you've done
> so far.
>
> Mark
>
> On Sun, Dec 24, 2017, 07:24 MD <refmac5 at gmail.com> wrote:
>
> > Hi Gromacs folks,
> >
> > I want to look at protein peptide interaction. After docking two
> > conformations of the peptide emerged, and both of which make chemistry
> > sense and have similar low binding energies. (+-1 kj/mol). The distance
> > between the two conformations of the peptide is ~8A.
> >
> > Then I tried simulations on the two scenarios of protein peptide
> complexes
> > and the results showed the peptide only shifted very slightly in both
> > simulations. The rmsd, and energy dropping are all similar. I wonder if
> > there are other ways to make a judgement to tell which conformation of
> the
> > peptide makes more sense by analyzing their MD results?
> >
> > Thanks,
> >
> > Ming
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