[gmx-users] simulation time vs side chain flexibility

[Justin Lemkul]

On 2/20/18 12:16 PM, MD wrote:
> Thanks J. I agree. I should have added that the RMSD plateaued. And I am

Don't let RMSD lull you into a false sense of security. If your side 
chain gets "stuck" in one conformation, its RMSD will be low, but it 
tells you nothing about its flexibility because there are no reversible 
transitions. Moreover, RMSD is a degenerate metrics that does not tell 
you anything about the actual convergence of your simulation. It may be 
a first indicator in many cases, but it is not definitive by any means.

RMSF is very sensitive to proper equilibration. I normally discard at 
least 10-20 ns of simulation time before trusting my RMSF results (which 
are then independently monitored for their own convergence in 
non-overlapping windows of time).

-Justin

> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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