[gmx-users] simulation time vs side chain flexibility

[MD]

Thank you J.
Ming

On Tue, Feb 20, 2018 at 12:29 PM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> To be honest, I don't see how an increased side chain flexibility is proof
> that the protein is more flexible. They're not necessarily correlated.
> Protein flexibility involves larger movements concerning the protein
> backbone. These would probably be better captured by the RMSF, radius or
> gyration, end-to-end distance, etc.
>
> J
>
> On Tue, Feb 20, 2018 at 6:16 PM, MD <refmac5 at gmail.com> wrote:
>
> > Thanks J. I agree. I should have added that the RMSD plateaued. And I am
> > more looking at side chain flexibility instead of secondary structure
> > changes.
> > Ming
> >
> > On Tue, Feb 20, 2018 at 12:09 PM, João Henriques <
> > joao.m.a.henriques at gmail.com> wrote:
> >
> > > This is not strictly a gromacs related question, but long answer short:
> > it
> > > depends, but most likely not. You must be able to convince people that
> > the
> > > property you're interested in is properly converged within the
> simulation
> > > time you're considering. Multiple, reversible events need to be clearly
> > > visible.
> > >
> > > In general, significant protein conformational changes occur at a much
> > > larger time scale (and I'm talking orders of magnitude larger). 10 ns
> is
> > a
> > > very, very short time for most purposes in protein simulation.
> > >
> > > I could go on and on, this is a complex topic that can easily be
> written
> > > about at length.
> > >
> > > J
> > >
> > > On Tue, Feb 20, 2018 at 5:48 PM, MD <refmac5 at gmail.com> wrote:
> > >
> > > > Hi Gromacs folks,
> > > >
> > > > I am trying to tell if a mutation can cause some part of the protein
> > > > becoming more flexible. I started with the apo protein. I did two
> > > > simulations in parallel, with one wild type and one with a silico
> > > mutation.
> > > >
> > > > After a 10 ns simulation I was able to tell some region of the
> protein
> > is
> > > > more flexible based on the RMS chart. Since side chain flexibility is
> > in
> > > > the range of 1 ns, I wonder if 10 ns simulation is convincing enough?
> > > >
> > > > Thanks,
> > > >
> > > > Ming
> > > > --
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