[gmx-users] simulation time vs side chain flexibility

[João Henriques]

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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