[gmx-users] Validation of molecular dynamic simulation results

[João Henriques]

First of all, please address me in a casual manner, "Sir" makes me feel old
and I'm just in my mid 20's :)

Now I'll try to be as less verbose as I can, because I think there's a
little communication issue here.

Authenticity usually points out towards originality, something not copied,
genuine. I knew you meant something different and thus my previous remark.

You don't have to tell us the full story behind the study you're doing.
This mailing list serves to help people with difficulties regarding the
gromacs software package. Your difficulty lies elsewhere, ie. you want
someone to tell you what to do next in your project. *That is a scientific
decision not a technical issue*, if you understand what I mean. It's
something you have to discuss with your research group and
collaborators. Unless you come to me with a concrete idea for an
analysis/study I'm afraid I can't help you.

Don't take this personally, but I simply can not do your "homework" in
full. *Come to me with a concrete idea like, "I want to measure how
dissimilar A and B are" or "I want to know how I can compute this and
that", etc, and then I (or someone else) might be able to assist you.*

Best regards,
João



On Tue, Feb 11, 2014 at 12:43 PM, ananyachatterjee <
ananyachatterjee at iiserkol.ac.in> wrote:

> Dear Sir,
>
> My protein contains two domain and upon GTP hydrolysis, the protein under
> goes conformational change and it shows inter-domain movement. I did few
> biochemical test which showed me that the upon a mutation in the conserved
> residue (which is localed in the chain connecting the two domain)the GTPase
> activity is reduced and also it has effected the cell growth. Now to see
> whether the mutation is some how effecting the inter domain movement of the
> protein(which is a important property of the protein for it function) I
> performed the simulations keeping the parameters close to the biochemical
> experiments(like con. of ions, temp. etc) . Now when I presented my work in
> a conference people asked me about its authenticity, how much close it is
> to the reality and whether it is reproducible. I want to know how to verify
> my simulations.
>
> Thanks in advance
>
>
> On Tue, 11 Feb 2014 11:24:53 +0100, João Henriques wrote:
>
>> 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
>>>>>
>>>>> * 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
>>>>>
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>>>>> 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,
>>> IISER-Kolkata.
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
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>>>
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>>>
>>>
> --
> 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!
>
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>
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>