[gmx-users] Validation of molecular dynamic simulation results

ananyachatterjee ananyachatterjee at iiserkol.ac.in
Tue Feb 11 09:46:33 CET 2014

 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
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 
>> or
>> send a mail to gmx-users-request at gromacs.org.

 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,

More information about the gromacs.org_gmx-users mailing list