[gmx-users] simulation time vs side chain flexibility

[MD]

Thank you Justin.
Ming

On Tue, Feb 20, 2018 at 12:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> 303 Engel Hall
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> jalemkul at vt.edu | (540) 231-3129
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