[gmx-users] Validation of molecular dynamic simulation results

[João Henriques]

Dear Ananya,

Sorry but I don't understand what you're saying. What do you mean by "molecular
movement of my protein"? Do you mean diffusion? Please be more specific.
You also mention "authenticity", but I don't think that's what you meant...

You have done PCA, RMSD and RMSF analyses. That's nice and all, but do you
have a reason for doing them? What I meant with my previous email is
that *there
is no fixed recipe that one must always follow in order to validate their
simulations*. The analyses your simulation requires in order to be
validated depend on the simulation purpose and what experimental data you
have to compare them to.

Take this overly simplistic example: Imagine I've performed a simple
"protein in water" MD simulation. The protein is well behaved (stable
native structure) and there is a high resolution experimental structure of
it. Radius of gyration, RMSD, RMSF and DSSP analyses would be good
candidates to show whether my force field, settings and parameters are
adequate or not in maintaining the well known native 3D structure.

Like I said before, you're the one that must be familiar with your system,
simulation and overall project aim. I am happy to help you in identifying
the tool you need to perform a certain analysis/study or even helping
understanding any error or problem with it. However I cannot do your own
work in identifying what needs to be done and where you're heading.

Best regards,
João


On Tue, Feb 11, 2014 at 9:46 AM, ananyachatterjee <
ananyachatterjee at iiserkol.ac.in> wrote:

> On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote:
>
>> Dear Ananya,
>>
>> Shouldn't this be something you already had in mind even before attempting
>> to simulate? Usually, a simulation is a means to an end. What is your end,
>> ie. what made you do this simulation? The motivation behind your
>> simulation
>> is usually what will determine what type of validation it requires. Sure,
>> there are quasi-standard analysis and sanity checks that one almost always
>> uses to ensure the simulation is relevant, but you can find those in any
>> given MD tutorial available online. For this, Google is your friend and
>> you
>> also have quite popular tutorials such as Justin's for example:
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
>>
>> I suggest you sit down and think a bit about what are you attempting to
>> achieve with your simulation. Pinpoint what type of analysis you need and
>> then take a careful look at the Gromacs manual. There you will find all
>> you
>> need to know about the analysis tools available to you. They're not
>> guaranteed to cover all your needs, but they usually more than suffice in
>> providing what most researchers need to validate their simulations.
>>
>> Best regards,
>> João
>>
>>
>> On Tue, Feb 11, 2014 at 8:02 AM, ananyachatterjee <
>> ananyachatterjee at iiserkol.ac.in> wrote:
>>
>>  Hello everyone,
>>>
>>> I have done a set of molecular dynamic simulation of my protein and its
>>> mutated structure, now please tell me how should I validate the
>>> simulation
>>> results or structures. Whether I can reproduce the same simulations.
>>>
>>> Thank you in advance
>>>
>>> --
>>> Ananya Chatterjee,
>>> Senior Research Fellow (SRF),
>>> Department of biological Science,
>>> IISER-Kolkata.
>>> --
>>> Gromacs Users mailing list
>>>
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>>>
> Dear João,
>
> Thank you for your reply, I was intended to seen the difference in
> molecular movement of my protein upon mutation. My protein is a GTPase
> protein and I have done simulation in presence of GTP, GDP and GDP+Pi for
> both the wild type and the mutated protein. Then I have done principle
> component analysis and RMSD & RMSF comparison of the trajectories. Now I
> want to check the authenticity of the set of simulation and whether they
> can be reproduce to validate my results.
>
> Please kindly help me in this regard.
>
> --
> Ananya Chatterjee,
> Senior Research Fellow (SRF),
> Department of biological Science,
> IISER-Kolkata.
> --
> Gromacs Users mailing list
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