[gmx-users] Validation of molecular dynamic simulation results

[João Henriques]

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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