[gmx-users] simulation time vs side chain flexibility

João Henriques joao.m.a.henriques at gmail.com
Tue Feb 20 18:09:50 CET 2018

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

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.


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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