[gmx-users] Validation of molecular dynamic simulation results

[ananyachatterjee]

 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.
>> --
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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.