[gmx-users] simulation time vs side chain flexibility

[MD]

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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