[gmx-users] Periodic Images - clarification

[Tsjerk Wassenaar]

Hey,

Maybe I missed this, but what type of unit cell did you use? You
should use a rhombic dodecahedron.

Then, I would argue that it isn't necessarily so problematic as the
others put it when you have transient contacts. For the greater part
of the simulation the distances in the periodic system are so large
that there can be no direct effect between opposite ends of the
protein. It is unlikely that the brief periods where the opposite ends
were within each others sphere of influence - not in contact - would
have caused a persistent deviation from in ensemble. Mind that it's
not wrong that a protein would suddenly feel some presence from some
end of a similar protein some distance away at some time. It's just
wrong if a protein aligns with itself. That has not happened if these
minimal distances were only transient. It may well be that the protein
was going from one conformation to another, for which it had to go
through something that would violate the PBC a bit. Still, you are in
for some discussion, and have to argue, based on what the simulation
shows you, what (a) replicate simulation(s) show(s) you and what you
know of your protein, why it would be justified to draw conclusions
based on that trajectory.

But those are just my two cents.

Cheers,

Tsjerk

On Sun, Jun 26, 2011 at 5:41 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Kavyashree M wrote:
>>
>> Sir,
>>  I would like to thank you for patiently replying for my repeatedly asked
>> question.
>>
>>
>>    For most stable, well-behaved proteins, setting a suitable box size
>>    at the outset of the simulation is sufficient to avoid spurious PBC
>>    interactions.  In your case, there are several possibilities: (1)
>>    the protein is not well-behaved, (2) you didn't set the box you
>>    think you did, (3) the .mdp settings are wrong and lead to
>>    instability, or (4) your pressure coupling settings cause the box to
>>    shrink unreasonably.
>>
>>  1. protein is not well behaved - This point I dont know how to quantify.
>
> It's not necessarily something you can quantify, it's more of a qualitative
> measure in many cases and comes from anticipating what the system may do.
>  Not all proteins are stably folded.  Some may unfold, others may have
> multiple domains that will move along hinge regions, causing the protein to
> expand its size, etc.  The initial box size assumes that large changes in
> the structure will not occur.  Sometimes this assumption is not good.
>
>> 2. Box dimensions - I repeated from the model, editconf gave the same box
>> dimensions which I had used earlier but did not      repeat the NVT. and the
>> distance -d between wall of box and protein atom was kept as 1.0nm while the
>> max cut of used was
>>   1.4nm.
>> 3. I am attaching the mdp file.
>> 4. I checked the whole trajectory for change in box size with the output
>> of g_energy. But did not find and abrupt deviations
>>
>
> OK.
>
>>
>>    If you want to use the first 26 ns only, I suppose these data are
>>    legitimate, although then several questions arise.  Why did you run
>>    100 ns in the first place?  Presumably you felt that you needed such
>>    a simulation length to address whatever question you're asking, so
>>    is 26 ns legitimate, or is it simply convenient because you don't
>>    want to run the simulation again?  Also, why trust these results
>>    when you know that just a short time later these dynamics produced
>>    flawed information?  The PBC violation may not have simply happened
>>    suddenly; maybe it was a product of some long-term motion in the
>>    system that was continually trending towards disaster.
>>
>>  I did not anticipate such a violation would as it did not happen in other
>> cases. so I did not check the minimum image violation
>> while running the simulation but caculated after 100ns. I agree it was my
>> stupidity. Because of time constraints and system unavailability now I might
>> not be able to run another simulation. But I will be running it later with
>> corrected parameters for sure.
>>
>> I agree that it is producing flawed results. But My point was if at all it
>> was caused only due to the box dimension being smaller
>> and not due to any wrong parameters used why is that 26ns wrong. Probably
>> if I had selected a bigger box size may be that
>> loop would have continued to move without minimum image violation.
>>
>>    The biggest question is, if you run the simulation again (which you
>>    should, but only after answering the four points above and the
>>    following), how do you know the same thing won't happen again?
>>     You've been asking related questions for weeks and I still do not
>>    know if you have followed my repeated advice to watch the trajectory
>>    with a PBC unit cell enabled in your favorite visualization program
>>    and, in concert with the identified problematic atoms in the
>>    g_mindist output, identify where and why the minimum image violation
>>    occurred.  Doing so should take minutes and you should immediately
>>    see what went wrong, which would be valuable information for
>>    avoiding such behavior in the future.  If you have done this, you've
>>    posted no evidence of your findings and thus just wasted weeks
>>    posting the same (or tangentially related) questions with no answer,
>>    time that could have been spent running a proper simulation to
>>    recover what you lost.
>>
>>
>> If I am running again I would increase the box size and run. I did what
>> you had suggested.  I visualized that part of trajectory
>> in VMD (which I am not very comfortable with ) and could see a loop
>> movement coming closer to it periodic image. but
>> unfortunately because of my lack of know-how I was unable to measure the
>> distance between them in VMD. I could only visualixe the loop movement but I
>> am unable to produce and concrete outputs for my observation.
>>
>
> It seems you have identified the source of the problem then.  If you have a
> large, unpredictable loop region, then you need to account for the fact that
> it might do funny things throughout the simulation.  In this case, maybe
> your 26 ns is useful, but my point is that if you thought 100 ns was needed
> to answer your question of interest, then you still probably need to do a
> new simulation.
>
> Also realize that the results of just a single simulation is usually not
> sufficient to derive converged quantities.  What if your one simulation is
> the outlier in the sample set?  You have no way to know if you've done just
> one simulation.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands